[{"scopus_import":"1","article_processing_charge":"Yes","has_accepted_license":"1","day":"13","citation":{"chicago":"Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2220075121.","mla":"Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 7, e2220075121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2220075121.","short":"S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 121(7), e2220075121.","ieee":"S. Curk et al., “Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 7. Proceedings of the National Academy of Sciences, 2024.","apa":"Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C. T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2220075121","ama":"Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(7). doi:10.1073/pnas.2220075121"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_type":"original","date_published":"2024-02-13T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer’s A\r\n amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A\r\n fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15001","intvolume":" 121","title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","status":"public","ddc":["570"],"file":[{"access_level":"open_access","file_name":"2024_PNAS_Curk.pdf","content_type":"application/pdf","file_size":7699487,"creator":"dernst","relation":"main_file","file_id":"15026","checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b","success":1,"date_updated":"2024-02-26T08:20:00Z","date_created":"2024-02-26T08:20:00Z"}],"oa_version":"Published Version","publication_identifier":{"eissn":["1091-6490"]},"month":"02","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["38335256"]},"project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020"}],"quality_controlled":"1","doi":"10.1073/pnas.2220075121","language":[{"iso":"eng"}],"article_number":"e2220075121","ec_funded":1,"file_date_updated":"2024-02-26T08:20:00Z","pmid":1,"year":"2024","acknowledgement":"We acknowledge support from the Erasmus programme and the University College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K., S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C. and A.Š.).","department":[{"_id":"AnSa"}],"publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","related_material":{"record":[{"id":"15027","relation":"research_data","status":"public"}]},"author":[{"first_name":"Samo","last_name":"Curk","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","orcid":"0000-0001-6160-9766","full_name":"Curk, Samo"},{"last_name":"Krausser","first_name":"Johannes","full_name":"Krausser, Johannes"},{"last_name":"Meisl","first_name":"Georg","full_name":"Meisl, Georg"},{"full_name":"Frenkel, Daan","first_name":"Daan","last_name":"Frenkel"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"full_name":"Michaels, Thomas C.T.","last_name":"Michaels","first_name":"Thomas C.T."},{"full_name":"Knowles, Tuomas P.J.","last_name":"Knowles","first_name":"Tuomas P.J."},{"first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"}],"volume":121,"date_updated":"2024-02-26T08:45:56Z","date_created":"2024-02-18T23:01:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevLett.132.050401","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2201.10220","open_access":"1"}],"external_id":{"arxiv":["2201.10220"]},"publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"month":"01","volume":132,"date_created":"2024-02-18T23:01:00Z","date_updated":"2024-02-26T08:03:31Z","author":[{"id":"0ac84990-897b-11ed-a09c-f5abb56a4ede","last_name":"Petrova","first_name":"Elena","full_name":"Petrova, Elena"},{"full_name":"Tiunov, Egor S.","last_name":"Tiunov","first_name":"Egor S."},{"first_name":"Mari Carmen","last_name":"Bañuls","full_name":"Bañuls, Mari Carmen"},{"last_name":"Fedorov","first_name":"Aleksey K.","full_name":"Fedorov, Aleksey K."}],"publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_status":"published","year":"2024","acknowledgement":"We thank A. Bargov, I. Khaymovich, and V. Tiunova for fruitful discussions and for useful comments. M. C. B. thanks S. Kühn for discussions about the phase structure of the model. A. K. F. thanks V. Gritsev and A. Garkun for insightful comments. E. V. P., E. S. T., and A. K. F. are\r\nsupported by the RSF Grant No. 20-42-05002 (studying the fractal Ansatz) and the Roadmap on Quantum Computing (Contract No. 868-1.3-15/15-2021, October 5, 2021; calculating on GS energies). A. K. F. thanks the Priority 2030 program at the NIST “MISIS” under the project No. K1-2022-027. M. C. B. was partly funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC-2111–390814868.","article_number":"050401","date_published":"2024-01-30T00:00:00Z","article_type":"original","citation":{"ista":"Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. 2024. Fractal states of the Schwinger model. Physical Review Letters. 132(5), 050401.","apa":"Petrova, E., Tiunov, E. S., Bañuls, M. C., & Fedorov, A. K. (2024). Fractal states of the Schwinger model. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.132.050401","ieee":"E. Petrova, E. S. Tiunov, M. C. Bañuls, and A. K. Fedorov, “Fractal states of the Schwinger model,” Physical Review Letters, vol. 132, no. 5. American Physical Society, 2024.","ama":"Petrova E, Tiunov ES, Bañuls MC, Fedorov AK. Fractal states of the Schwinger model. Physical Review Letters. 2024;132(5). doi:10.1103/PhysRevLett.132.050401","chicago":"Petrova, Elena, Egor S. Tiunov, Mari Carmen Bañuls, and Aleksey K. Fedorov. “Fractal States of the Schwinger Model.” Physical Review Letters. American Physical Society, 2024. https://doi.org/10.1103/PhysRevLett.132.050401.","mla":"Petrova, Elena, et al. “Fractal States of the Schwinger Model.” Physical Review Letters, vol. 132, no. 5, 050401, American Physical Society, 2024, doi:10.1103/PhysRevLett.132.050401.","short":"E. Petrova, E.S. Tiunov, M.C. Bañuls, A.K. Fedorov, Physical Review Letters 132 (2024)."},"publication":"Physical Review Letters","article_processing_charge":"No","day":"30","scopus_import":"1","oa_version":"Preprint","intvolume":" 132","title":"Fractal states of the Schwinger model","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15002","issue":"5","abstract":[{"lang":"eng","text":"The lattice Schwinger model, the discrete version of QED in \r\n1\r\n+\r\n1\r\n dimensions, is a well-studied test bench for lattice gauge theories. Here, we study the fractal properties of this model. We reveal the self-similarity of the ground state, which allows us to develop a recurrent procedure for finding the ground-state wave functions and predicting ground-state energies. We present the results of recurrently calculating ground-state wave functions using the fractal Ansatz and automized software package for fractal image processing. In certain parameter regimes, just a few terms are enough for our recurrent procedure to predict ground-state energies close to the exact ones for several hundreds of sites. Our findings pave the way to understanding the complexity of calculating many-body wave functions in terms of their fractal properties as well as finding new links between condensed matter and high-energy lattice models."}],"type":"journal_article"},{"abstract":[{"lang":"eng","text":"In this paper we introduce the critical variational setting for parabolic stochastic evolution equations of quasi- or semi-linear type. Our results improve many of the abstract results in the classical variational setting. In particular, we are able to replace the usual weak or local monotonicity condition by a more flexible local Lipschitz condition. Moreover, the usual growth conditions on the multiplicative noise are weakened considerably. Our new setting provides general conditions under which local and global existence and uniqueness hold. Moreover, we prove continuous dependence on the initial data. We show that many classical SPDEs, which could not be covered by the classical variational setting, do fit in the critical variational setting. In particular, this is the case for the Cahn-Hilliard equations, tamed Navier-Stokes equations, and Allen-Cahn equation."}],"type":"journal_article","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12485","title":"The critical variational setting for stochastic evolution equations","status":"public","day":"02","article_processing_charge":"No","scopus_import":"1","date_published":"2024-02-02T00:00:00Z","publication":"Probability Theory and Related Fields","citation":{"ista":"Agresti A, Veraar M. 2024. The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields.","apa":"Agresti, A., & Veraar, M. (2024). The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields. Springer Nature. https://doi.org/10.1007/s00440-023-01249-x","ieee":"A. Agresti and M. Veraar, “The critical variational setting for stochastic evolution equations,” Probability Theory and Related Fields. Springer Nature, 2024.","ama":"Agresti A, Veraar M. The critical variational setting for stochastic evolution equations. Probability Theory and Related Fields. 2024. doi:10.1007/s00440-023-01249-x","chicago":"Agresti, Antonio, and Mark Veraar. “The Critical Variational Setting for Stochastic Evolution Equations.” Probability Theory and Related Fields. Springer Nature, 2024. https://doi.org/10.1007/s00440-023-01249-x.","mla":"Agresti, Antonio, and Mark Veraar. “The Critical Variational Setting for Stochastic Evolution Equations.” Probability Theory and Related Fields, Springer Nature, 2024, doi:10.1007/s00440-023-01249-x.","short":"A. Agresti, M. Veraar, Probability Theory and Related Fields (2024)."},"article_type":"original","ec_funded":1,"author":[{"full_name":"Agresti, Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","first_name":"Antonio","last_name":"Agresti"},{"full_name":"Veraar, Mark","first_name":"Mark","last_name":"Veraar"}],"date_updated":"2024-02-26T09:39:07Z","date_created":"2023-02-02T10:45:15Z","year":"2024","acknowledgement":"The first author has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 948819) . The second author is supported by the VICI subsidy VI.C.212.027 of the Netherlands Organisation for Scientific Research (NWO).","publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"JuFi"}],"month":"02","publication_identifier":{"eissn":["1432-2064"],"issn":["0178-8051"]},"doi":"10.1007/s00440-023-01249-x","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2206.00230"]},"main_file_link":[{"url":"https://doi.org/10.1007/s00440-023-01249-x","open_access":"1"}],"quality_controlled":"1","project":[{"_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","grant_number":"948819","call_identifier":"H2020","name":"Bridging Scales in Random Materials"}]},{"department":[{"_id":"MoHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","acknowledgement":"Monika Henzinger and A. R. Sricharan: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation\r\nprogramme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) project Z\r\n422-N, project I 5982-N, and project P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nHarald Räcke: Research supported by German Research Foundation (DFG), grant 470029389\r\n(FlexNets), 2021-2024.\r\nSushant Sachdeva: SS’s work is supported by an Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Grant RGPIN-2018-06398 and a Sloan Research Fellowship.","year":"2024","volume":287,"date_updated":"2024-02-26T10:12:19Z","date_created":"2024-02-18T23:01:02Z","author":[{"first_name":"Gramoz","last_name":"Goranci","full_name":"Goranci, Gramoz"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Harald","last_name":"Räcke","full_name":"Räcke, Harald"},{"last_name":"Sachdeva","first_name":"Sushant","full_name":"Sachdeva, Sushant"},{"full_name":"Sricharan, A. R.","last_name":"Sricharan","first_name":"A. R."}],"article_number":"55","ec_funded":1,"file_date_updated":"2024-02-26T10:10:48Z","project":[{"name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Wittgenstein Award - Monika Henzinger"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2303.02491"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.ITCS.2024.55","conference":{"location":"Berkeley, CA, United States","start_date":"2024-01-30","end_date":"2024-02-02","name":"ITCS: Innovations in Theoretical Computer Science Conference"},"publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773096"]},"month":"01","intvolume":" 287","ddc":["000"],"status":"public","title":"Electrical flows for polylogarithmic competitive oblivious routing","_id":"15008","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"b89716aae6a5599f187897e39de1e53a","success":1,"date_created":"2024-02-26T10:10:48Z","date_updated":"2024-02-26T10:10:48Z","relation":"main_file","file_id":"15030","content_type":"application/pdf","file_size":1054754,"creator":"dernst","access_level":"open_access","file_name":"2024_LIPICs_Goranci.pdf"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"Oblivious routing is a well-studied paradigm that uses static precomputed routing tables for selecting routing paths within a network. Existing oblivious routing schemes with polylogarithmic competitive ratio for general networks are tree-based, in the sense that routing is performed according to a convex combination of trees. However, this restriction to trees leads to a construction that has time quadratic in the size of the network and does not parallelize well. \r\nIn this paper we study oblivious routing schemes based on electrical routing. In particular, we show that general networks with n vertices and m edges admit a routing scheme that has competitive ratio O(log² n) and consists of a convex combination of only O(√m) electrical routings. This immediately leads to an improved construction algorithm with time Õ(m^{3/2}) that can also be implemented in parallel with Õ(√m) depth.","lang":"eng"}],"citation":{"chicago":"Goranci, Gramoz, Monika H Henzinger, Harald Räcke, Sushant Sachdeva, and A. R. Sricharan. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” In 15th Innovations in Theoretical Computer Science Conference, Vol. 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.ITCS.2024.55.","short":"G. Goranci, M.H. Henzinger, H. Räcke, S. Sachdeva, A.R. Sricharan, in:, 15th Innovations in Theoretical Computer Science Conference, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Goranci, Gramoz, et al. “Electrical Flows for Polylogarithmic Competitive Oblivious Routing.” 15th Innovations in Theoretical Computer Science Conference, vol. 287, 55, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.ITCS.2024.55.","apa":"Goranci, G., Henzinger, M. H., Räcke, H., Sachdeva, S., & Sricharan, A. R. (2024). Electrical flows for polylogarithmic competitive oblivious routing. In 15th Innovations in Theoretical Computer Science Conference (Vol. 287). Berkeley, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.ITCS.2024.55","ieee":"G. Goranci, M. H. Henzinger, H. Räcke, S. Sachdeva, and A. R. Sricharan, “Electrical flows for polylogarithmic competitive oblivious routing,” in 15th Innovations in Theoretical Computer Science Conference, Berkeley, CA, United States, 2024, vol. 287.","ista":"Goranci G, Henzinger MH, Räcke H, Sachdeva S, Sricharan AR. 2024. Electrical flows for polylogarithmic competitive oblivious routing. 15th Innovations in Theoretical Computer Science Conference. ITCS: Innovations in Theoretical Computer Science Conference, LIPIcs, vol. 287, 55.","ama":"Goranci G, Henzinger MH, Räcke H, Sachdeva S, Sricharan AR. Electrical flows for polylogarithmic competitive oblivious routing. In: 15th Innovations in Theoretical Computer Science Conference. Vol 287. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.ITCS.2024.55"},"publication":"15th Innovations in Theoretical Computer Science Conference","date_published":"2024-01-24T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"24"},{"month":"01","publication_identifier":{"isbn":["9783959773089"],"issn":["1868-8969"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2023-12-08","start_date":"2023-12-06","location":"Tokyo, Japan","name":"OPODIS: Conference on Principles of Distributed Systems"},"doi":"10.4230/LIPIcs.OPODIS.2023.12","quality_controlled":"1","external_id":{"arxiv":["2307.02954"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"file_date_updated":"2024-02-26T10:16:57Z","article_number":"12","date_updated":"2024-02-26T10:18:18Z","date_created":"2024-02-18T23:01:02Z","volume":286,"author":[{"first_name":"Orestis","last_name":"Alpos","full_name":"Alpos, Orestis"},{"first_name":"Ignacio","last_name":"Amores-Sesar","full_name":"Amores-Sesar, Ignacio"},{"full_name":"Cachin, Christian","first_name":"Christian","last_name":"Cachin"},{"full_name":"Yeo, Michelle X","last_name":"Yeo","first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"KrPi"}],"year":"2024","acknowledgement":"We would like to thank Krzysztof Pietrzak and Jovana Mićić for useful discussions. This work has been funded by the Swiss National Science Foundation (SNSF) under grant agreement Nr. 200021_188443 (Advanced Consensus Protocols).\r\n","day":"18","has_accepted_license":"1","article_processing_charge":"No","scopus_import":"1","date_published":"2024-01-18T00:00:00Z","publication":"27th International Conference on Principles of Distributed Systems","citation":{"chicago":"Alpos, Orestis, Ignacio Amores-Sesar, Christian Cachin, and Michelle X Yeo. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering Attacks.” In 27th International Conference on Principles of Distributed Systems, Vol. 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.OPODIS.2023.12.","short":"O. Alpos, I. Amores-Sesar, C. Cachin, M.X. Yeo, in:, 27th International Conference on Principles of Distributed Systems, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Alpos, Orestis, et al. “Eating Sandwiches: Modular and Lightweight Elimination of Transaction Reordering Attacks.” 27th International Conference on Principles of Distributed Systems, vol. 286, 12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.OPODIS.2023.12.","apa":"Alpos, O., Amores-Sesar, I., Cachin, C., & Yeo, M. X. (2024). Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. In 27th International Conference on Principles of Distributed Systems (Vol. 286). Tokyo, Japan: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.OPODIS.2023.12","ieee":"O. Alpos, I. Amores-Sesar, C. Cachin, and M. X. Yeo, “Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks,” in 27th International Conference on Principles of Distributed Systems, Tokyo, Japan, 2024, vol. 286.","ista":"Alpos O, Amores-Sesar I, Cachin C, Yeo MX. 2024. Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. 27th International Conference on Principles of Distributed Systems. OPODIS: Conference on Principles of Distributed Systems, LIPIcs, vol. 286, 12.","ama":"Alpos O, Amores-Sesar I, Cachin C, Yeo MX. Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks. In: 27th International Conference on Principles of Distributed Systems. Vol 286. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.OPODIS.2023.12"},"abstract":[{"text":"Traditional blockchains grant the miner of a block full control not only over which transactions but also their order. This constitutes a major flaw discovered with the introduction of decentralized finance and allows miners to perform MEV attacks. In this paper, we address the issue of sandwich attacks by providing a construction that takes as input a blockchain protocol and outputs a new blockchain protocol with the same security but in which sandwich attacks are not profitable. Furthermore, our protocol is fully decentralized with no trusted third parties or heavy cryptography primitives and carries a linear increase in latency and minimum computation overhead.","lang":"eng"}],"alternative_title":["LIPIcs"],"type":"conference","oa_version":"Published Version","file":[{"file_id":"15031","relation":"main_file","date_updated":"2024-02-26T10:16:57Z","date_created":"2024-02-26T10:16:57Z","success":1,"checksum":"2993e810a45e8c8056106834b07aea92","file_name":"2024_LIPICs_Alpos.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":1505994}],"ddc":["000"],"title":"Eating sandwiches: Modular and lightweight elimination of transaction reordering attacks","status":"public","intvolume":" 286","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15007"},{"abstract":[{"text":"For a set of points in Rd, the Euclidean k-means problems consists of finding k centers such that the sum of distances squared from each data point to its closest center is minimized. Coresets are one the main tools developed recently to solve this problem in a big data context. They allow to compress the initial dataset while preserving its structure: running any algorithm on the coreset provides a guarantee almost equivalent to running it on the full data. In this work, we study coresets in a fully-dynamic setting: points are added and deleted with the goal to efficiently maintain a coreset with which a k-means solution can be computed. Based on an algorithm from Henzinger and Kale [ESA'20], we present an efficient and practical implementation of a fully dynamic coreset algorithm, that improves the running time by up to a factor of 20 compared to our non-optimized implementation of the algorithm by Henzinger and Kale, without sacrificing more than 7% on the quality of the k-means solution.","lang":"eng"}],"type":"conference","oa_version":"Preprint","_id":"14769","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Experimental evaluation of fully dynamic k-means via coresets","status":"public","day":"04","article_processing_charge":"No","scopus_import":"1","date_published":"2024-01-04T00:00:00Z","publication":"2024 Proceedings of the Symposium on Algorithm Engineering and Experiments","citation":{"ama":"Henzinger MH, Saulpic D, Sidl L. Experimental evaluation of fully dynamic k-means via coresets. In: 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments. Society for Industrial & Applied Mathematics; 2024:220-233. doi:10.1137/1.9781611977929.17","ista":"Henzinger MH, Saulpic D, Sidl L. 2024. Experimental evaluation of fully dynamic k-means via coresets. 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments. ALENEX: Workshop on Algorithm Engineering and Experiments, 220–233.","apa":"Henzinger, M. H., Saulpic, D., & Sidl, L. (2024). Experimental evaluation of fully dynamic k-means via coresets. In 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments (pp. 220–233). Alexandria, VA, United States: Society for Industrial & Applied Mathematics. https://doi.org/10.1137/1.9781611977929.17","ieee":"M. H. Henzinger, D. Saulpic, and L. Sidl, “Experimental evaluation of fully dynamic k-means via coresets,” in 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Alexandria, VA, United States, 2024, pp. 220–233.","mla":"Henzinger, Monika H., et al. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Society for Industrial & Applied Mathematics, 2024, pp. 220–33, doi:10.1137/1.9781611977929.17.","short":"M.H. Henzinger, D. Saulpic, L. Sidl, in:, 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, Society for Industrial & Applied Mathematics, 2024, pp. 220–233.","chicago":"Henzinger, Monika H, David Saulpic, and Leonhard Sidl. “Experimental Evaluation of Fully Dynamic K-Means via Coresets.” In 2024 Proceedings of the Symposium on Algorithm Engineering and Experiments, 220–33. Society for Industrial & Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977929.17."},"page":"220-233","ec_funded":1,"author":[{"full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"last_name":"Saulpic","first_name":"David","id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","full_name":"Saulpic, David"},{"id":"8b563fd0-b441-11ee-9101-a3891c61efa6","first_name":"Leonhard","last_name":"Sidl","full_name":"Sidl, Leonhard"}],"date_created":"2024-01-09T16:22:47Z","date_updated":"2024-02-26T09:51:31Z","acknowledgement":"This project has received funding from the Euro-pean Research Council (ERC) under the EuropeanUnion’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The De-sign of Modern Fully Dynamic Data Structures (Mo-DynStruct)” and the Austrian Science Fund (FWF)project Z 422-N, project “Static and Dynamic Hierar-chical Graph Decompositions”, I 5982-N, and project“Fast Algorithms for a Reactive Network Layer (Re-actNet)”, P 33775-N, with additional funding from thenetidee SCIENCE Stiftung, 2020–2024.D. Sauplic has received funding from the Euro-pean Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreementNo 101034413.","year":"2024","publication_status":"published","department":[{"_id":"MoHe"}],"publisher":"Society for Industrial & Applied Mathematics","month":"01","publication_identifier":{"eisbn":["9781611977929"]},"conference":{"name":"ALENEX: Workshop on Algorithm Engineering and Experiments","end_date":"2024-01-08","location":"Alexandria, VA, United States","start_date":"2024-01-07"},"doi":"10.1137/1.9781611977929.17","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.18034"}],"external_id":{"arxiv":["2310.18034"]},"quality_controlled":"1","project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Wittgenstein Award - Monika Henzinger"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"},{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}]},{"day":"20","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2024-01-20T00:00:00Z","article_type":"original","publication":"Genome Biology and Evolution","citation":{"chicago":"Bett, Vincent K, Ariana Macon, Beatriz Vicoso, and Marwan N Elkrewi. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution. Oxford University Press, 2024. https://doi.org/10.1093/gbe/evae006.","short":"V.K. Bett, A. Macon, B. Vicoso, M.N. Elkrewi, Genome Biology and Evolution 16 (2024).","mla":"Bett, Vincent K., et al. “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex Chromosome Differentiation.” Genome Biology and Evolution, vol. 16, no. 1, evae006, Oxford University Press, 2024, doi:10.1093/gbe/evae006.","apa":"Bett, V. K., Macon, A., Vicoso, B., & Elkrewi, M. N. (2024). Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evae006","ieee":"V. K. Bett, A. Macon, B. Vicoso, and M. N. Elkrewi, “Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation,” Genome Biology and Evolution, vol. 16, no. 1. Oxford University Press, 2024.","ista":"Bett VK, Macon A, Vicoso B, Elkrewi MN. 2024. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 16(1), evae006.","ama":"Bett VK, Macon A, Vicoso B, Elkrewi MN. Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation. Genome Biology and Evolution. 2024;16(1). doi:10.1093/gbe/evae006"},"abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, is still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of A. franciscana (Kellogg 1906), from the Great Salt Lake, United States. The genome is 1 GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2024_GBE_Bett.pdf","file_size":5213306,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"15029","checksum":"106a40f10443b2e7ba66749844ebbdf1","success":1,"date_updated":"2024-02-26T09:54:59Z","date_created":"2024-02-26T09:54:59Z"}],"ddc":["570"],"title":"Chromosome-level assembly of Artemia franciscana sheds light on sex chromosome differentiation","status":"public","intvolume":" 16","_id":"15009","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","publication_identifier":{"eissn":["1759-6653"]},"language":[{"iso":"eng"}],"doi":"10.1093/gbe/evae006","quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38245839"]},"file_date_updated":"2024-02-26T09:54:59Z","article_number":"evae006","date_created":"2024-02-18T23:01:02Z","date_updated":"2024-02-26T09:59:30Z","volume":16,"author":[{"first_name":"Vincent K","last_name":"Bett","id":"57854184-AAE0-11E9-8D04-98D6E5697425","full_name":"Bett, Vincent K"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","first_name":"Ariana","full_name":"Macon, Ariana"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"},{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"14705"}]},"publication_status":"published","publisher":"Oxford University Press","department":[{"_id":"BeVi"}],"year":"2024","pmid":1},{"oa_version":"Preprint","_id":"15004","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics","intvolume":" 109","abstract":[{"lang":"eng","text":"The impulsive limit (the “sudden approximation”) has been widely employed to describe the interaction between molecules and short, far-off-resonant laser pulses. This approximation assumes that the timescale of the laser-molecule interaction is significantly shorter than the internal rotational period of the molecule, resulting in the rotational motion being instantaneously “frozen” during the interaction. This simplified description of the laser-molecule interaction is incorporated in various theoretical models predicting rotational dynamics of molecules driven by short laser pulses. In this theoretical work, we develop an effective theory for ultrashort laser pulses by examining the full time-evolution operator and solving the time-dependent Schrödinger equation at the operator level. Our findings reveal a critical angular momentum, lcrit, at which the impulsive limit breaks down. In other words, the validity of the sudden approximation depends not only on the pulse duration but also on its intensity, since the latter determines how many angular momentum states are populated. We explore both ultrashort multicycle (Gaussian) pulses and the somewhat less studied half-cycle pulses, which produce distinct effective potentials. We discuss the limitations of the impulsive limit and propose a method that rescales the effective matrix elements, enabling an improved and more accurate description of laser-molecule interactions."}],"issue":"2","type":"journal_article","date_published":"2024-02-01T00:00:00Z","publication":"Physical Review A","citation":{"mla":"Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” Physical Review A, vol. 109, no. 2, 023101, American Physical Society, 2024, doi:10.1103/PhysRevA.109.023101.","short":"V. Karle, M. Lemeshko, Physical Review A 109 (2024).","chicago":"Karle, Volker, and Mikhail Lemeshko. “Modeling Laser Pulses as δ Kicks: Reevaluating the Impulsive Limit in Molecular Rotational Dynamics.” Physical Review A. American Physical Society, 2024. https://doi.org/10.1103/PhysRevA.109.023101.","ama":"Karle V, Lemeshko M. Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. 2024;109(2). doi:10.1103/PhysRevA.109.023101","ista":"Karle V, Lemeshko M. 2024. Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. 109(2), 023101.","ieee":"V. Karle and M. Lemeshko, “Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics,” Physical Review A, vol. 109, no. 2. American Physical Society, 2024.","apa":"Karle, V., & Lemeshko, M. (2024). Modeling laser pulses as δ kicks: Reevaluating the impulsive limit in molecular rotational dynamics. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.109.023101"},"article_type":"original","day":"01","article_processing_charge":"No","scopus_import":"1","author":[{"orcid":"0000-0002-6963-0129","id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","last_name":"Karle","first_name":"Volker","full_name":"Karle, Volker"},{"full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-26T09:45:20Z","date_created":"2024-02-18T23:01:01Z","volume":109,"year":"2024","acknowledgement":"We thank Bretislav Friedrich, Marjan Mirahmadi, Artem Volosniev, and Burkhard Schmidt for insightful discussions. M.L. acknowledges support by the European Research Council (ERC) under Starting Grant No. 801770 (ANGULON).","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","ec_funded":1,"article_number":"023101","doi":"10.1103/PhysRevA.109.023101","language":[{"iso":"eng"}],"external_id":{"arxiv":["2307.07256"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2307.07256"}],"oa":1,"quality_controlled":"1","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"}],"month":"02","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]}},{"publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"ddc":["576"],"title":"Data from \"Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation\"","status":"public","_id":"14705","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2024","file":[{"file_id":"14707","relation":"main_file","success":1,"checksum":"bdaf1392867786634ec5466d528c36ca","date_created":"2023-12-22T13:54:21Z","date_updated":"2023-12-22T13:54:21Z","access_level":"open_access","file_name":"readme.txt.txt","creator":"melkrewi","content_type":"text/plain","file_size":847},{"date_created":"2023-12-22T14:14:06Z","date_updated":"2023-12-22T14:14:06Z","checksum":"973e1cbdab923a71709782177980829f","success":1,"relation":"main_file","file_id":"14708","content_type":"application/x-zip-compressed","file_size":343632753,"creator":"melkrewi","file_name":"data_artemia_franciscana_genome.zip","access_level":"open_access"}],"oa_version":"Published Version","date_updated":"2024-02-26T09:59:29Z","date_created":"2023-12-22T13:40:48Z","related_material":{"record":[{"id":"15009","status":"public","relation":"used_in_publication"}]},"contributor":[{"id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K","contributor_type":"researcher","last_name":"Bett"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","last_name":"Macon","contributor_type":"project_member","first_name":"Ariana"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","first_name":"Beatriz","contributor_type":"supervisor","last_name":"Vicoso"},{"contributor_type":"researcher","last_name":"Elkrewi","first_name":"Marwan N","orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"}],"author":[{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","last_name":"Elkrewi","first_name":"Marwan N","full_name":"Elkrewi, Marwan N"}],"type":"research_data","file_date_updated":"2023-12-22T14:14:06Z","abstract":[{"text":"Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species.","lang":"eng"}],"project":[{"name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","grant_number":"F8810"}],"citation":{"chicago":"Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:14705.","short":"M.N. Elkrewi, (2024).","mla":"Elkrewi, Marwan N. Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:14705.","ieee":"M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024.","apa":"Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14705","ista":"Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14705.","ama":"Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:10.15479/AT:ISTA:14705"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"date_published":"2024-01-02T00:00:00Z","doi":"10.15479/AT:ISTA:14705","keyword":["sex chromosome evolution","genome assembly","dosage compensation"],"has_accepted_license":"1","article_processing_charge":"No","month":"01","day":"02"},{"issue":"5","abstract":[{"lang":"eng","text":"Magnetic frustration allows to access novel and intriguing properties of magnetic systems and has been explored mainly in planar triangular-like arrays of magnetic ions. In this work, we describe the phosphide Ce6Ni6P17, where the Ce+3 ions accommodate in a body-centered cubic lattice of Ce6 regular octahedra. From measurements of magnetization, specific heat, and resistivity, we determine a rich phase diagram as a function of temperature and magnetic field in which different magnetic phases are found. Besides clear evidence of magnetic frustration is obtained from entropy analysis. At zero field, a second-order antiferromagnetic transition occurs at TN1≈1 K followed by a first-order transition at TN2≈0.45 K. With magnetic field new magnetic phases appear, including a weakly first-order transition which ends in a classical critical point and a third magnetic phase. We also study the exact solution of the spin-1/2 Heisenberg model in an octahedron which allows us a qualitative understanding of the phase diagram and compare with the experimental results."}],"type":"journal_article","oa_version":"None","_id":"15003","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 109","title":"Frustrated magnetism in octahedra-based Ce6 Ni6 P17","status":"public","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2024-02-01T00:00:00Z","citation":{"chicago":"Franco, D. G., R. Avalos, D. Hafner, Kimberly A Modic, Yu Prots, O. Stockert, A. Hoser, et al. “Frustrated Magnetism in Octahedra-Based Ce6 Ni6 P17.” Physical Review B. American Physical Society, 2024. https://doi.org/10.1103/PhysRevB.109.054405.","short":"D.G. Franco, R. Avalos, D. Hafner, K.A. Modic, Y. Prots, O. Stockert, A. Hoser, P.J.W. Moll, M. Brando, A.A. Aligia, C. Geibel, Physical Review B 109 (2024).","mla":"Franco, D. G., et al. “Frustrated Magnetism in Octahedra-Based Ce6 Ni6 P17.” Physical Review B, vol. 109, no. 5, 054405, American Physical Society, 2024, doi:10.1103/PhysRevB.109.054405.","apa":"Franco, D. G., Avalos, R., Hafner, D., Modic, K. A., Prots, Y., Stockert, O., … Geibel, C. (2024). Frustrated magnetism in octahedra-based Ce6 Ni6 P17. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.109.054405","ieee":"D. G. Franco et al., “Frustrated magnetism in octahedra-based Ce6 Ni6 P17,” Physical Review B, vol. 109, no. 5. American Physical Society, 2024.","ista":"Franco DG, Avalos R, Hafner D, Modic KA, Prots Y, Stockert O, Hoser A, Moll PJW, Brando M, Aligia AA, Geibel C. 2024. Frustrated magnetism in octahedra-based Ce6 Ni6 P17. Physical Review B. 109(5), 054405.","ama":"Franco DG, Avalos R, Hafner D, et al. Frustrated magnetism in octahedra-based Ce6 Ni6 P17. Physical Review B. 2024;109(5). doi:10.1103/PhysRevB.109.054405"},"publication":"Physical Review B","article_type":"original","article_number":"054405","author":[{"full_name":"Franco, D. G.","first_name":"D. G.","last_name":"Franco"},{"full_name":"Avalos, R.","first_name":"R.","last_name":"Avalos"},{"full_name":"Hafner, D.","first_name":"D.","last_name":"Hafner"},{"full_name":"Modic, Kimberly A","orcid":"0000-0001-9760-3147","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","last_name":"Modic","first_name":"Kimberly A"},{"first_name":"Yu","last_name":"Prots","full_name":"Prots, Yu"},{"full_name":"Stockert, O.","last_name":"Stockert","first_name":"O."},{"full_name":"Hoser, A.","first_name":"A.","last_name":"Hoser"},{"full_name":"Moll, P. J.W.","first_name":"P. J.W.","last_name":"Moll"},{"first_name":"M.","last_name":"Brando","full_name":"Brando, M."},{"full_name":"Aligia, A. A.","last_name":"Aligia","first_name":"A. A."},{"last_name":"Geibel","first_name":"C.","full_name":"Geibel, C."}],"volume":109,"date_created":"2024-02-18T23:01:01Z","date_updated":"2024-02-26T09:50:10Z","acknowledgement":"The authors thank Bernardo Pentke for the SEM micrographs (Departamento Fisicoquímica de Materiales CABCNEA). We are indebted to Julián Sereni for useful discussions. D. G. F. acknowledges financial support provided by Agencia I+D+i, Argentina, Grant No. PICT-2021-I-INVI00852 and Universidad Nacional de Cuyo (SIIP) Grant No. 06/C018-T1. A. A. A. acknowledges financial support provided by PICT 2018-01546 and PICT 2020A-03661 of the\r\nAgencia I+D+i. ","year":"2024","publisher":"American Physical Society","department":[{"_id":"KiMo"}],"publication_status":"published","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"02","doi":"10.1103/PhysRevB.109.054405","language":[{"iso":"eng"}],"quality_controlled":"1"},{"oa_version":"Published Version","intvolume":" 174","title":"Compressively strained epitaxial Ge layers for quantum computing applications","ddc":["530"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15018","issue":"5","abstract":[{"text":"The epitaxial growth of a strained Ge layer, which is a promising candidate for the channel material of a hole spin qubit, has been demonstrated on 300 mm Si wafers using commercially available Si0.3Ge0.7 strain relaxed buffer (SRB) layers. The assessment of the layer and the interface qualities for a buried strained Ge layer embedded in Si0.3Ge0.7 layers is reported. The XRD reciprocal space mapping confirmed that the reduction of the growth temperature enables the 2-dimensional growth of the Ge layer fully strained with respect to the Si0.3Ge0.7. Nevertheless, dislocations at the top and/or bottom interface of the Ge layer were observed by means of electron channeling contrast imaging, suggesting the importance of the careful dislocation assessment. The interface abruptness does not depend on the selection of the precursor gases, but it is strongly influenced by the growth temperature which affects the coverage of the surface H-passivation. The mobility of 2.7 × 105 cm2/Vs is promising, while the low percolation density of 3 × 1010 /cm2 measured with a Hall-bar device at 7 K illustrates the high quality of the heterostructure thanks to the high Si0.3Ge0.7 SRB quality.","lang":"eng"}],"type":"journal_article","date_published":"2024-02-20T00:00:00Z","article_type":"original","citation":{"short":"Y. Shimura, C. Godfrin, A. Hikavyy, R. Li, J.L. Aguilera Servin, G. Katsaros, P. Favia, H. Han, D. Wan, K. de Greve, R. Loo, Materials Science in Semiconductor Processing 174 (2024).","mla":"Shimura, Yosuke, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing, vol. 174, no. 5, 108231, Elsevier, 2024, doi:10.1016/j.mssp.2024.108231.","chicago":"Shimura, Yosuke, Clement Godfrin, Andriy Hikavyy, Roy Li, Juan L Aguilera Servin, Georgios Katsaros, Paola Favia, et al. “Compressively Strained Epitaxial Ge Layers for Quantum Computing Applications.” Materials Science in Semiconductor Processing. Elsevier, 2024. https://doi.org/10.1016/j.mssp.2024.108231.","ama":"Shimura Y, Godfrin C, Hikavyy A, et al. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 2024;174(5). doi:10.1016/j.mssp.2024.108231","ieee":"Y. Shimura et al., “Compressively strained epitaxial Ge layers for quantum computing applications,” Materials Science in Semiconductor Processing, vol. 174, no. 5. Elsevier, 2024.","apa":"Shimura, Y., Godfrin, C., Hikavyy, A., Li, R., Aguilera Servin, J. L., Katsaros, G., … Loo, R. (2024). Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. Elsevier. https://doi.org/10.1016/j.mssp.2024.108231","ista":"Shimura Y, Godfrin C, Hikavyy A, Li R, Aguilera Servin JL, Katsaros G, Favia P, Han H, Wan D, de Greve K, Loo R. 2024. Compressively strained epitaxial Ge layers for quantum computing applications. Materials Science in Semiconductor Processing. 174(5), 108231."},"publication":"Materials Science in Semiconductor Processing","article_processing_charge":"No","has_accepted_license":"1","day":"20","keyword":["Mechanical Engineering","Mechanics of Materials","Condensed Matter Physics","General Materials Science"],"volume":174,"date_created":"2024-02-22T14:10:40Z","date_updated":"2024-02-26T10:36:35Z","author":[{"first_name":"Yosuke","last_name":"Shimura","full_name":"Shimura, Yosuke"},{"full_name":"Godfrin, Clement","last_name":"Godfrin","first_name":"Clement"},{"last_name":"Hikavyy","first_name":"Andriy","full_name":"Hikavyy, Andriy"},{"first_name":"Roy","last_name":"Li","full_name":"Li, Roy"},{"full_name":"Aguilera Servin, Juan L","last_name":"Aguilera Servin","first_name":"Juan L","orcid":"0000-0002-2862-8372","id":"2A67C376-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"},{"full_name":"Favia, Paola","last_name":"Favia","first_name":"Paola"},{"full_name":"Han, Han","first_name":"Han","last_name":"Han"},{"last_name":"Wan","first_name":"Danny","full_name":"Wan, Danny"},{"full_name":"de Greve, Kristiaan","last_name":"de Greve","first_name":"Kristiaan"},{"first_name":"Roger","last_name":"Loo","full_name":"Loo, Roger"}],"department":[{"_id":"GeKa"},{"_id":"NanoFab"}],"publisher":"Elsevier","publication_status":"epub_ahead","acknowledgement":"The Ge project received funding from the European Union's Horizon Europe programme under the Grant Agreement 101069515 – IGNITE. Siltronic AG is acknowledged for providing the SRB wafers. This work was supported by Imec's Industrial Affiliation Program on Quantum Computing.","year":"2024","article_number":"108231","language":[{"iso":"eng"}],"doi":"10.1016/j.mssp.2024.108231","project":[{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515","name":"Integrated GermaNIum quanTum tEchnology"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"url":"https://doi.org/10.1016/j.mssp.2024.108231","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["1369-8001"]},"month":"02"},{"alternative_title":["PMLR"],"type":"conference","abstract":[{"lang":"eng","text":"Pruning large language models (LLMs) from the BERT family has emerged as a standard compression benchmark, and several pruning methods have been proposed for this task. The recent “Sparsity May Cry” (SMC) benchmark put into question the validity of all existing methods, exhibiting a more complex setup where many known pruning methods appear to fail. We revisit the question of accurate BERT-pruning during fine-tuning on downstream datasets, and propose a set of general guidelines for successful pruning, even on the challenging SMC benchmark. First, we perform a cost-vs-benefits analysis of pruning model components, such as the embeddings and the classification head; second, we provide a simple-yet-general way of scaling training, sparsification and learning rate schedules relative to the desired target sparsity; finally, we investigate the importance of proper parametrization for Knowledge Distillation in the context of LLMs. Our simple insights lead to state-of-the-art results, both on classic BERT-pruning benchmarks, as well as on the SMC benchmark, showing that even classic gradual magnitude pruning (GMP) can yield competitive results, with the right approach."}],"intvolume":" 234","title":"How to prune your language model: Recovering accuracy on the \"Sparsity May Cry\" benchmark","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15011","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"08","page":"542-553","citation":{"chicago":"Kurtic, Eldar, Torsten Hoefler, and Dan-Adrian Alistarh. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” In Proceedings of Machine Learning Research, 234:542–53. ML Research Press, 2024.","short":"E. Kurtic, T. Hoefler, D.-A. Alistarh, in:, Proceedings of Machine Learning Research, ML Research Press, 2024, pp. 542–553.","mla":"Kurtic, Eldar, et al. “How to Prune Your Language Model: Recovering Accuracy on the ‘Sparsity May Cry’ Benchmark.” Proceedings of Machine Learning Research, vol. 234, ML Research Press, 2024, pp. 542–53.","ieee":"E. Kurtic, T. Hoefler, and D.-A. Alistarh, “How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark,” in Proceedings of Machine Learning Research, Hongkong, China, 2024, vol. 234, pp. 542–553.","apa":"Kurtic, E., Hoefler, T., & Alistarh, D.-A. (2024). How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In Proceedings of Machine Learning Research (Vol. 234, pp. 542–553). Hongkong, China: ML Research Press.","ista":"Kurtic E, Hoefler T, Alistarh D-A. 2024. How to prune your language model: Recovering accuracy on the ‘Sparsity May Cry’ benchmark. Proceedings of Machine Learning Research. CPAL: Conference on Parsimony and Learning, PMLR, vol. 234, 542–553.","ama":"Kurtic E, Hoefler T, Alistarh D-A. How to prune your language model: Recovering accuracy on the “Sparsity May Cry” benchmark. In: Proceedings of Machine Learning Research. Vol 234. ML Research Press; 2024:542-553."},"publication":"Proceedings of Machine Learning Research","date_published":"2024-01-08T00:00:00Z","publisher":"ML Research Press","department":[{"_id":"DaAl"}],"publication_status":"published","year":"2024","volume":234,"date_updated":"2024-02-26T10:30:52Z","date_created":"2024-02-18T23:01:03Z","author":[{"id":"47beb3a5-07b5-11eb-9b87-b108ec578218","first_name":"Eldar","last_name":"Kurtic","full_name":"Kurtic, Eldar"},{"full_name":"Hoefler, Torsten","first_name":"Torsten","last_name":"Hoefler"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","first_name":"Dan-Adrian"}],"publication_identifier":{"eissn":["2640-3498"]},"month":"01","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://proceedings.mlr.press/v234/kurtic24a"}],"external_id":{"arxiv":["2312.13547"]},"language":[{"iso":"eng"}],"conference":{"name":"CPAL: Conference on Parsimony and Learning","end_date":"2024-01-06","location":"Hongkong, China","start_date":"2024-01-03"}},{"day":"14","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_published":"2024-02-14T00:00:00Z","publication":"Journal of Chemical Physics","citation":{"short":"P. Robin, Journal of Chemical Physics 160 (2024).","mla":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:10.1063/5.0188215.","chicago":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0188215.","ama":"Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 2024;160(6). doi:10.1063/5.0188215","ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” Journal of Chemical Physics, vol. 160, no. 6. AIP Publishing, 2024.","apa":"Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0188215","ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503."},"article_type":"original","abstract":[{"text":"Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions.","lang":"eng"}],"issue":"6","type":"journal_article","oa_version":"Published Version","file":[{"checksum":"0a5e0ae70849bce674466fc054390ec0","success":1,"date_created":"2024-02-27T08:12:52Z","date_updated":"2024-02-27T08:12:52Z","relation":"main_file","file_id":"15034","content_type":"application/pdf","file_size":5452738,"creator":"dernst","access_level":"open_access","file_name":"2024_JourChemicalPhysics_Robin.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15024","title":"Correlation-induced viscous dissipation in concentrated electrolytes","ddc":["540"],"status":"public","intvolume":" 160","month":"02","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"doi":"10.1063/5.0188215","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2311.11784"],"pmid":["38349632"]},"quality_controlled":"1","project":[{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"}],"file_date_updated":"2024-02-27T08:12:52Z","ec_funded":1,"article_number":"064503","author":[{"full_name":"Robin, Paul","first_name":"Paul","last_name":"Robin","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","orcid":"0000-0002-5728-9189"}],"date_created":"2024-02-25T23:00:55Z","date_updated":"2024-02-27T08:16:06Z","volume":160,"acknowledgement":"The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu Lizée for fruitful discussions. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","year":"2024","pmid":1,"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"AIP Publishing"},{"month":"02","publication_identifier":{"issn":["1050-5164"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2208.12206","open_access":"1"}],"external_id":{"arxiv":["2208.12206"]},"quality_controlled":"1","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"doi":"10.1214/23-AAP2000","language":[{"iso":"eng"}],"ec_funded":1,"acknowledgement":"The first author was supported by the ERC Advanced Grant “RMTBeyond” No. 101020331. The second author was supported by Fulbright Austria and the Austrian Marshall Plan Foundation.","year":"2024","publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"Erdös, László"},{"id":"b0cc634c-d549-11ee-96c8-87338c7ad808","orcid":"0000-0003-2625-495X","first_name":"Benjamin","last_name":"McKenna","full_name":"McKenna, Benjamin"}],"date_created":"2024-02-25T23:00:56Z","date_updated":"2024-02-27T08:29:05Z","volume":34,"scopus_import":"1","day":"01","article_processing_charge":"No","publication":"Annals of Applied Probability","citation":{"short":"L. Erdös, B. McKenna, Annals of Applied Probability 34 (2024) 1623–1662.","mla":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” Annals of Applied Probability, vol. 34, no. 1B, Institute of Mathematical Statistics, 2024, pp. 1623–62, doi:10.1214/23-AAP2000.","chicago":"Erdös, László, and Benjamin McKenna. “Extremal Statistics of Quadratic Forms of GOE/GUE Eigenvectors.” Annals of Applied Probability. Institute of Mathematical Statistics, 2024. https://doi.org/10.1214/23-AAP2000.","ama":"Erdös L, McKenna B. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 2024;34(1B):1623-1662. doi:10.1214/23-AAP2000","ieee":"L. Erdös and B. McKenna, “Extremal statistics of quadratic forms of GOE/GUE eigenvectors,” Annals of Applied Probability, vol. 34, no. 1B. Institute of Mathematical Statistics, pp. 1623–1662, 2024.","apa":"Erdös, L., & McKenna, B. (2024). Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-AAP2000","ista":"Erdös L, McKenna B. 2024. Extremal statistics of quadratic forms of GOE/GUE eigenvectors. Annals of Applied Probability. 34(1B), 1623–1662."},"article_type":"original","page":"1623-1662","date_published":"2024-02-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We consider quadratic forms of deterministic matrices A evaluated at the random eigenvectors of a large N×N GOE or GUE matrix, or equivalently evaluated at the columns of a Haar-orthogonal or Haar-unitary random matrix. We prove that, as long as the deterministic matrix has rank much smaller than √N, the distributions of the extrema of these quadratic forms are asymptotically the same as if the eigenvectors were independent Gaussians. This reduces the problem to Gaussian computations, which we carry out in several cases to illustrate our result, finding Gumbel or Weibull limiting distributions depending on the signature of A. Our result also naturally applies to the eigenvectors of any invariant ensemble."}],"issue":"1B","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15025","status":"public","title":"Extremal statistics of quadratic forms of GOE/GUE eigenvectors","intvolume":" 34","oa_version":"Preprint"},{"language":[{"iso":"eng"}],"doi":"10.7554/elife.68993","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.7554/eLife.68993"}],"publication_identifier":{"issn":["2050-084X"]},"month":"02","volume":13,"date_updated":"2024-02-28T12:29:43Z","date_created":"2024-02-27T07:10:11Z","author":[{"full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","last_name":"Adamowski","first_name":"Maciek"},{"id":"83c17ce3-15b2-11ec-abd3-f486545870bd","last_name":"Matijevic","first_name":"Ivana","full_name":"Matijevic, Ivana"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"JiFr"}],"publisher":"eLife Sciences Publications","publication_status":"epub_ahead","acknowledgement":"The authors would like to gratefully acknowledge Dr Xixi Zhang for cloning the GNL1/pDONR221 construct and for useful discussions.H2020 European Research\r\nCouncil Advanced Grant ETAP742985 to Jiří Friml, Austrian Science Fund I 3630-B25 to Jiří Friml","year":"2024","ec_funded":1,"date_published":"2024-02-21T00:00:00Z","article_type":"original","citation":{"mla":"Adamowski, Maciek, et al. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife, vol. 13, eLife Sciences Publications, 2024, doi:10.7554/elife.68993.","short":"M. Adamowski, I. Matijevic, J. Friml, ELife 13 (2024).","chicago":"Adamowski, Maciek, Ivana Matijevic, and Jiří Friml. “Developmental Patterning Function of GNOM ARF-GEF Mediated from the Cell Periphery.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.68993.","ama":"Adamowski M, Matijevic I, Friml J. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 2024;13. doi:10.7554/elife.68993","ista":"Adamowski M, Matijevic I, Friml J. 2024. Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. eLife. 13.","apa":"Adamowski, M., Matijevic, I., & Friml, J. (2024). Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.68993","ieee":"M. Adamowski, I. Matijevic, and J. Friml, “Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery,” eLife, vol. 13. eLife Sciences Publications, 2024."},"publication":"eLife","has_accepted_license":"1","article_processing_charge":"Yes","day":"21","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"oa_version":"Published Version","intvolume":" 13","ddc":["580"],"status":"public","title":"Developmental patterning function of GNOM ARF-GEF mediated from the cell periphery","_id":"15033","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The GNOM (GN) Guanine nucleotide Exchange Factor for ARF small GTPases (ARF-GEF) is among the best studied trafficking regulators in plants, playing crucial and unique developmental roles in patterning and polarity. The current models place GN at the Golgi apparatus (GA), where it mediates secretion/recycling, and at the plasma membrane (PM) presumably contributing to clathrin-mediated endocytosis (CME). The mechanistic basis of the developmental function of GN, distinct from the other ARF-GEFs including its closest homologue GNOM-LIKE1 (GNL1), remains elusive. Insights from this study largely extend the current notions of GN function. We show that GN, but not GNL1, localizes to the cell periphery at long-lived structures distinct from clathrin-coated pits, while CME and secretion proceed normally in gn knockouts. The functional GN mutant variant GNfewerroots, absent from the GA, suggests that the cell periphery is the major site of GN action responsible for its developmental function. Following inhibition by Brefeldin A, GN, but not GNL1, relocates to the PM likely on exocytic vesicles, suggesting selective molecular associations en route to the cell periphery. A study of GN-GNL1 chimeric ARF-GEFs indicates that all GN domains contribute to the specific GN function in a partially redundant manner. Together, this study offers significant steps toward the elucidation of the mechanism underlying unique cellular and development functions of GNOM.","lang":"eng"}],"type":"journal_article"},{"page":"902-909.e6","article_type":"original","citation":{"chicago":"Csata, Eniko, Alfonso Perez-Escudero, Emmanuel Laury, Hanna Leitner, Gerard Latil, Juerge Heinze, Stephen Simpson, Sylvia Cremer, and Audrey Dussutour. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2024.01.017.","short":"E. Csata, A. Perez-Escudero, E. Laury, H. Leitner, G. Latil, J. Heinze, S. Simpson, S. Cremer, A. Dussutour, Current Biology 34 (2024) 902–909.e6.","mla":"Csata, Eniko, et al. “Fungal Infection Alters Collective Nutritional Intake of Ant Colonies.” Current Biology, vol. 34, no. 4, Elsevier, 2024, p. 902–909.e6, doi:10.1016/j.cub.2024.01.017.","apa":"Csata, E., Perez-Escudero, A., Laury, E., Leitner, H., Latil, G., Heinze, J., … Dussutour, A. (2024). Fungal infection alters collective nutritional intake of ant colonies. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2024.01.017","ieee":"E. Csata et al., “Fungal infection alters collective nutritional intake of ant colonies,” Current Biology, vol. 34, no. 4. Elsevier, p. 902–909.e6, 2024.","ista":"Csata E, Perez-Escudero A, Laury E, Leitner H, Latil G, Heinze J, Simpson S, Cremer S, Dussutour A. 2024. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 34(4), 902–909.e6.","ama":"Csata E, Perez-Escudero A, Laury E, et al. Fungal infection alters collective nutritional intake of ant colonies. Current Biology. 2024;34(4):902-909.e6. doi:10.1016/j.cub.2024.01.017"},"publication":"Current Biology","date_published":"2024-02-26T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"26","intvolume":" 34","title":"Fungal infection alters collective nutritional intake of ant colonies","status":"public","_id":"14479","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","issue":"4","abstract":[{"text":"In animals, parasitic infections impose significant fitness costs.1,2,3,4,5,6 Infected animals can alter their feeding behavior to resist infection,7,8,9,10,11,12 but parasites can manipulate animal foraging behavior to their own benefits.13,14,15,16 How nutrition influences host-parasite interactions is not well understood, as studies have mainly focused on the host and less on the parasite.9,12,17,18,19,20,21,22,23 We used the nutritional geometry framework24 to investigate the role of amino acids (AA) and carbohydrates (C) in a host-parasite system: the Argentine ant, Linepithema humile, and the entomopathogenic fungus, Metarhizium brunneum. First, using 18 diets varying in AA:C composition, we established that the fungus performed best on the high-amino-acid diet 1:4. Second, we found that the fungus reached this optimal diet when given various diet pairings, revealing its ability to cope with nutritional challenges. Third, we showed that the optimal fungal diet reduced the lifespan of healthy ants when compared with a high-carbohydrate diet but had no effect on infected ants. Fourth, we revealed that infected ant colonies, given a choice between the optimal fungal diet and a high-carbohydrate diet, chose the optimal fungal diet, whereas healthy colonies avoided it. Lastly, by disentangling fungal infection from host immune response, we demonstrated that infected ants foraged on the optimal fungal diet in response to immune activation and not as a result of parasite manipulation. Therefore, we revealed that infected ant colonies chose a diet that is costly for survival in the long term but beneficial in the short term—a form of collective self-medication.","lang":"eng"}],"quality_controlled":"1","external_id":{"pmid":["38307022"]},"main_file_link":[{"url":"https://doi.org/10.1101/2023.10.26.564092","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2024.01.017","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"month":"02","department":[{"_id":"SyCr"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"year":"2024","acknowledgement":"We are sincerely grateful to the referees for their valuable comments and suggestions, which helped us to improve the paper. We are thankful to Jorgen Eilenberg and Nicolai V. Meyling for the fungal strain, to Simon Tragust, Abel Bernadou, and Brian Lazarro for insightful discussions, to Iago Sanmartín-Villar, Léa Briard, Céline Maitrel, and Nolwenn Rissen for their help with the experiments. Furthermore, we thank Anna V. Grasse for help with the immune gene expression analyses. We thank Sergio Ibarra for creating the graphical abstract. E.C. was supported by a Fyssen Foundation grant and the Alexander von Humboldt Foundation. A.D. was supported by the CNRS.","volume":34,"date_created":"2023-10-31T13:30:20Z","date_updated":"2024-03-04T07:14:41Z","author":[{"first_name":"Eniko","last_name":"Csata","full_name":"Csata, Eniko"},{"last_name":"Perez-Escudero","first_name":"Alfonso","full_name":"Perez-Escudero, Alfonso"},{"first_name":"Emmanuel","last_name":"Laury","full_name":"Laury, Emmanuel"},{"full_name":"Leitner, Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","last_name":"Leitner","first_name":"Hanna"},{"first_name":"Gerard","last_name":"Latil","full_name":"Latil, Gerard"},{"full_name":"Heinze, Juerge","first_name":"Juerge","last_name":"Heinze"},{"last_name":"Simpson","first_name":"Stephen","full_name":"Simpson, Stephen"},{"full_name":"Cremer, Sylvia","first_name":"Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868"},{"full_name":"Dussutour, Audrey","first_name":"Audrey","last_name":"Dussutour"}]},{"scopus_import":"1","keyword":["Atomic and Molecular Physics","and Optics"],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"17","citation":{"ista":"Varshney A, Ghazaryan A, Volosniev A. 2024. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 65, 12.","ieee":"A. Varshney, A. Ghazaryan, and A. Volosniev, “Classical ‘spin’ filtering with two degrees of freedom and dissipation,” Few-Body Systems, vol. 65. Springer Nature, 2024.","apa":"Varshney, A., Ghazaryan, A., & Volosniev, A. (2024). Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. Springer Nature. https://doi.org/10.1007/s00601-024-01880-x","ama":"Varshney A, Ghazaryan A, Volosniev A. Classical ‘spin’ filtering with two degrees of freedom and dissipation. Few-Body Systems. 2024;65. doi:10.1007/s00601-024-01880-x","chicago":"Varshney, Atul, Areg Ghazaryan, and Artem Volosniev. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems. Springer Nature, 2024. https://doi.org/10.1007/s00601-024-01880-x.","mla":"Varshney, Atul, et al. “Classical ‘Spin’ Filtering with Two Degrees of Freedom and Dissipation.” Few-Body Systems, vol. 65, 12, Springer Nature, 2024, doi:10.1007/s00601-024-01880-x.","short":"A. Varshney, A. Ghazaryan, A. Volosniev, Few-Body Systems 65 (2024)."},"publication":"Few-Body Systems","article_type":"original","date_published":"2024-02-17T00:00:00Z","type":"journal_article","abstract":[{"text":"Coupling of orbital motion to a spin degree of freedom gives rise to various transport phenomena in quantum systems that are beyond the standard paradigms of classical physics. Here, we discuss features of spin-orbit dynamics that can be visualized using a classical model with two coupled angular degrees of freedom. Specifically, we demonstrate classical ‘spin’ filtering through our model and show that the interplay between angular degrees of freedom and dissipation can lead to asymmetric ‘spin’ transport.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15045","intvolume":" 65","title":"Classical ‘spin’ filtering with two degrees of freedom and dissipation","status":"public","ddc":["530"],"oa_version":"Published Version","file":[{"file_name":"2024_FewBodySys_Varshney.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":436712,"file_id":"15049","relation":"main_file","date_updated":"2024-03-04T07:07:10Z","date_created":"2024-03-04T07:07:10Z","success":1,"checksum":"c4e08cc7bc756da69b1b36fda7bb92fb"}],"publication_identifier":{"issn":["1432-5411"]},"month":"02","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2401.08454"]},"quality_controlled":"1","doi":"10.1007/s00601-024-01880-x","language":[{"iso":"eng"}],"article_number":"12","file_date_updated":"2024-03-04T07:07:10Z","acknowledgement":"We thank Mikhail Lemeshko and members of his group for many inspiring discussions; Alberto Cappellaro for comments on the manuscript.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria).","year":"2024","publisher":"Springer Nature","department":[{"_id":"MiLe"}],"publication_status":"published","author":[{"full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","last_name":"Varshney","first_name":"Atul"},{"full_name":"Ghazaryan, Areg","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9666-3543","first_name":"Areg","last_name":"Ghazaryan"},{"full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"volume":65,"date_updated":"2024-03-04T07:08:16Z","date_created":"2024-03-01T11:39:33Z"},{"publication":"Physical Review Research","citation":{"chicago":"Jin, Shuwei, Kunlun Dai, Joris Verstraten, Maxime Dixmerias, Ragheed Al Hyder, Christophe Salomon, Bruno Peaudecerf, Tim de Jongh, and Tarik Yefsah. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013158.","short":"S. Jin, K. Dai, J. Verstraten, M. Dixmerias, R. Al Hyder, C. Salomon, B. Peaudecerf, T. de Jongh, T. Yefsah, Physical Review Research 6 (2024).","mla":"Jin, Shuwei, et al. “Multipurpose Platform for Analog Quantum Simulation.” Physical Review Research, vol. 6, no. 1, 013158, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013158.","ieee":"S. Jin et al., “Multipurpose platform for analog quantum simulation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","apa":"Jin, S., Dai, K., Verstraten, J., Dixmerias, M., Al Hyder, R., Salomon, C., … Yefsah, T. (2024). Multipurpose platform for analog quantum simulation. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013158","ista":"Jin S, Dai K, Verstraten J, Dixmerias M, Al Hyder R, Salomon C, Peaudecerf B, de Jongh T, Yefsah T. 2024. Multipurpose platform for analog quantum simulation. Physical Review Research. 6(1), 013158.","ama":"Jin S, Dai K, Verstraten J, et al. Multipurpose platform for analog quantum simulation. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013158"},"article_type":"original","date_published":"2024-02-13T00:00:00Z","scopus_import":"1","keyword":["General Physics and Astronomy"],"day":"13","article_processing_charge":"Yes","has_accepted_license":"1","_id":"15053","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"status":"public","title":"Multipurpose platform for analog quantum simulation","intvolume":" 6","file":[{"creator":"dernst","content_type":"application/pdf","file_size":4025988,"access_level":"open_access","file_name":"2024_PhysicalReviewResearch_Jin.pdf","success":1,"checksum":"ba2ae3e3a011f8897d3803c9366a67e2","date_updated":"2024-03-04T07:53:08Z","date_created":"2024-03-04T07:53:08Z","file_id":"15054","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Atom-based quantum simulators have had many successes in tackling challenging quantum many-body problems, owing to the precise and dynamical control that they provide over the systems' parameters. They are, however, often optimized to address a specific type of problem. Here, we present the design and implementation of a 6Li-based quantum gas platform that provides wide-ranging capabilities and is able to address a variety of quantum many-body problems. Our two-chamber architecture relies on a robust combination of gray molasses and optical transport from a laser-cooling chamber to a glass cell with excellent optical access. There, we first create unitary Fermi superfluids in a three-dimensional axially symmetric harmonic trap and characterize them using in situ thermometry, reaching temperatures below 20 nK. This allows us to enter the deep superfluid regime with samples of extreme diluteness, where the interparticle spacing is sufficiently large for direct single-atom imaging. Second, we generate optical lattice potentials with triangular and honeycomb geometry in which we study diffraction of molecular Bose-Einstein condensates, and show how going beyond the Kapitza-Dirac regime allows us to unambiguously distinguish between the two geometries. With the ability to probe quantum many-body physics in both discrete and continuous space, and its suitability for bulk and single-atom imaging, our setup represents an important step towards achieving a wide-scope quantum simulator.","lang":"eng"}],"issue":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2304.08433"]},"oa":1,"quality_controlled":"1","doi":"10.1103/physrevresearch.6.013158","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"issn":["2643-1564"]},"year":"2024","acknowledgement":"We thank Clara Bachorz, Darby Bates, Markus Bohlen, Valentin Crépel, Yann Kiefer, Joanna Lis, Mihail Rabinovic, and Julian Struck for experimental assistance in the early stages of this project, and Sebastian Will for a critical reading of the manuscript. This work has been supported by Agence Nationale de la Recherche (Grant No. ANR-21-CE30-0021), the European Research Council (Grant No. ERC-2016-ADG-743159), CNRS (Tremplin@INP 2020), and Région Ile-de-France in the framework of DIM SIRTEQ (Super2D and SISCo) and DIM QuanTiP.","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","author":[{"full_name":"Jin, Shuwei","first_name":"Shuwei","last_name":"Jin"},{"full_name":"Dai, Kunlun","first_name":"Kunlun","last_name":"Dai"},{"first_name":"Joris","last_name":"Verstraten","full_name":"Verstraten, Joris"},{"full_name":"Dixmerias, Maxime","first_name":"Maxime","last_name":"Dixmerias"},{"id":"d1c405be-ae15-11ed-8510-ccf53278162e","last_name":"Al Hyder","first_name":"Ragheed","full_name":"Al Hyder, Ragheed"},{"last_name":"Salomon","first_name":"Christophe","full_name":"Salomon, Christophe"},{"full_name":"Peaudecerf, Bruno","last_name":"Peaudecerf","first_name":"Bruno"},{"last_name":"de Jongh","first_name":"Tim","full_name":"de Jongh, Tim"},{"full_name":"Yefsah, Tarik","first_name":"Tarik","last_name":"Yefsah"}],"date_created":"2024-03-04T07:42:52Z","date_updated":"2024-03-04T07:55:29Z","volume":6,"article_number":"013158","file_date_updated":"2024-03-04T07:53:08Z"},{"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"month":"02","doi":"10.1242/dev.202316","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","call_identifier":"H2020"},{"name":"Mesendoderm specification in zebrafish: The role of extraembryonic tissues","grant_number":"25239","_id":"26B1E39C-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","ec_funded":1,"file_date_updated":"2024-03-04T07:24:43Z","related_material":{"record":[{"status":"public","relation":"research_data","id":"14926"}]},"author":[{"full_name":"Schauer, Alexandra","first_name":"Alexandra","last_name":"Schauer","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7659-9142"},{"id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija","last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"volume":151,"date_updated":"2024-03-04T07:28:25Z","date_created":"2024-03-03T23:00:50Z","year":"2024","acknowledgement":"We thank Patrick Müller for sharing the chordintt250 mutant zebrafish line as well as the plasmid for chrd-GFP, Katherine Rogers for sharing the bmp2b plasmid and Andrea Pauli for sharing the draculin plasmid. Diana Pinheiro generated the MZlefty1,2;Tg(sebox::EGFP) line. We are grateful to Patrick Müller, Diana Pinheiro and Katherine Rogers and members of the Heisenberg lab for discussions, technical advice and feedback on the manuscript. We also thank Anna Kicheva and Edouard Hannezo for discussions. We thank the Imaging and Optics Facility as well as the Life Science facility at IST Austria for support with microscopy and fish maintenance.\r\nThis work was supported by a European Research Council Advanced Grant\r\n(MECSPEC 742573 to C.-P.H.). A.S. is a recipient of a DOC Fellowship of the Austrian\r\nAcademy of Sciences at IST Austria. Open Access funding provided by Institute of\r\nScience and Technology Austria. ","publisher":"The Company of Biologists","department":[{"_id":"CaHe"},{"_id":"Bio"}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","scopus_import":"1","date_published":"2024-02-01T00:00:00Z","citation":{"apa":"Schauer, A., Pranjic-Ferscha, K., Hauschild, R., & Heisenberg, C.-P. J. (2024). Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. The Company of Biologists. https://doi.org/10.1242/dev.202316","ieee":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, and C.-P. J. Heisenberg, “Robust axis elongation by Nodal-dependent restriction of BMP signaling,” Development, vol. 151, no. 4. The Company of Biologists, pp. 1–18, 2024.","ista":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. 2024. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 151(4), 1–18.","ama":"Schauer A, Pranjic-Ferscha K, Hauschild R, Heisenberg C-PJ. Robust axis elongation by Nodal-dependent restriction of BMP signaling. Development. 2024;151(4):1-18. doi:10.1242/dev.202316","chicago":"Schauer, Alexandra, Kornelija Pranjic-Ferscha, Robert Hauschild, and Carl-Philipp J Heisenberg. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development. The Company of Biologists, 2024. https://doi.org/10.1242/dev.202316.","short":"A. Schauer, K. Pranjic-Ferscha, R. Hauschild, C.-P.J. Heisenberg, Development 151 (2024) 1–18.","mla":"Schauer, Alexandra, et al. “Robust Axis Elongation by Nodal-Dependent Restriction of BMP Signaling.” Development, vol. 151, no. 4, The Company of Biologists, 2024, pp. 1–18, doi:10.1242/dev.202316."},"publication":"Development","page":"1-18","article_type":"original","issue":"4","abstract":[{"lang":"eng","text":"Embryogenesis results from the coordinated activities of different signaling pathways controlling cell fate specification and morphogenesis. In vertebrate gastrulation, both Nodal and BMP signaling play key roles in germ layer specification and morphogenesis, yet their interplay to coordinate embryo patterning with morphogenesis is still insufficiently understood. Here, we took a reductionist approach using zebrafish embryonic explants to study the coordination of Nodal and BMP signaling for embryo patterning and morphogenesis. We show that Nodal signaling triggers explant elongation by inducing mesendodermal progenitors but also suppressing BMP signaling activity at the site of mesendoderm induction. Consistent with this, ectopic BMP signaling in the mesendoderm blocks cell alignment and oriented mesendoderm intercalations, key processes during explant elongation. Translating these ex vivo observations to the intact embryo showed that, similar to explants, Nodal signaling suppresses the effect of BMP signaling on cell intercalations in the dorsal domain, thus allowing robust embryonic axis elongation. These findings suggest a dual function of Nodal signaling in embryonic axis elongation by both inducing mesendoderm and suppressing BMP effects in the dorsal portion of the mesendoderm."}],"type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"6961ea10012bf0d266681f9628bb8f13","date_created":"2024-03-04T07:24:43Z","date_updated":"2024-03-04T07:24:43Z","file_id":"15050","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":14839986,"access_level":"open_access","file_name":"2024_Development_Schauer.pdf"}],"_id":"15048","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 151","status":"public","ddc":["570"],"title":"Robust axis elongation by Nodal-dependent restriction of BMP signaling"},{"date_published":"2024-02-14T00:00:00Z","article_type":"original","citation":{"apa":"Cheng, R., Zeng, Z., Wang, C., Ouyang, N., & Chen, Y. (2024). Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.109.054305","ieee":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, and Y. Chen, “Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites,” Physical Review B, vol. 109, no. 5. American Physical Society, 2024.","ista":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. 2024. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 109(5), 054305.","ama":"Cheng R, Zeng Z, Wang C, Ouyang N, Chen Y. Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites. Physical Review B. 2024;109(5). doi:10.1103/physrevb.109.054305","chicago":"Cheng, Ruihuan, Zezhu Zeng, Chen Wang, Niuchang Ouyang, and Yue Chen. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” Physical Review B. American Physical Society, 2024. https://doi.org/10.1103/physrevb.109.054305.","short":"R. Cheng, Z. Zeng, C. Wang, N. Ouyang, Y. Chen, Physical Review B 109 (2024).","mla":"Cheng, Ruihuan, et al. “Impact of Strain-Insensitive Low-Frequency Phonon Modes on Lattice Thermal Transport in AxXB6-Type Perovskites.” Physical Review B, vol. 109, no. 5, 054305, American Physical Society, 2024, doi:10.1103/physrevb.109.054305."},"publication":"Physical Review B","article_processing_charge":"No","day":"14","scopus_import":"1","oa_version":"None","intvolume":" 109","status":"public","title":"Impact of strain-insensitive low-frequency phonon modes on lattice thermal transport in AxXB6-type perovskites","_id":"15052","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"5","abstract":[{"lang":"eng","text":"Substrate induces mechanical strain on perovskite devices, which can result in alterations to its lattice dynamics and thermal transport. Herein, we have performed a theoretical investigation on the anharmonic lattice dynamics and thermal property of perovskite Rb2SnBr6 and Cs2SnBr6 under strains using perturbation theory up to the fourth-order terms and the unified thermal transport theory. We demonstrate a pronounced hardening of low-frequency optical phonons as temperature increases, indicating strong lattice anharmonicity and the necessity of adopting temperature-dependent interatomic force constants in the lattice thermal conductivity (\r\nκL) calculations. It is found that the low-lying optical phonon modes of Rb2SnBr6 are extremely soft and their phonon energies are almost strain independent, which ultimately lead to a lower \r\nκL and a weaker strain dependence than Cs2SnBr6. We further reveal that the strain dependence of these phonon modes in the A2XB6-type perovskites weakens as their ibrational frequency decreases. This study deepens the understanding of lattice thermal transport in perovskites A2XB6 and provides a perspective on the selection of materials that meet the expected thermal behaviors in practical applications."}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1103/physrevb.109.054305","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"quality_controlled":"1","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"02","volume":109,"date_updated":"2024-03-04T07:48:55Z","date_created":"2024-03-04T07:41:23Z","author":[{"last_name":"Cheng","first_name":"Ruihuan","full_name":"Cheng, Ruihuan"},{"full_name":"Zeng, Zezhu","id":"54a2c730-803f-11ed-ab7e-95b29d2680e7","first_name":"Zezhu","last_name":"Zeng"},{"full_name":"Wang, Chen","last_name":"Wang","first_name":"Chen"},{"last_name":"Ouyang","first_name":"Niuchang","full_name":"Ouyang, Niuchang"},{"first_name":"Yue","last_name":"Chen","full_name":"Chen, Yue"}],"publisher":"American Physical Society","department":[{"_id":"BiCh"}],"publication_status":"published","year":"2024","acknowledgement":"This work is supported by the Research Grants Council of Hong Kong (C7002-22Y and 17318122). The authors are grateful for the research computing facilities offered by\r\nITS, HKU. Z.Z. acknowledges the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","ec_funded":1,"article_number":"054305"},{"oa":1,"tmp":{"name":"The MIT License","legal_code_url":"https://opensource.org/licenses/MIT","short":"MIT"},"citation":{"mla":"Hauschild, Robert. Matlab Script for Analysis of Clone Dispersal. ISTA, 2024, doi:10.15479/AT:ISTA:14926.","short":"R. Hauschild, (2024).","chicago":"Hauschild, Robert. “Matlab Script for Analysis of Clone Dispersal.” ISTA, 2024. https://doi.org/10.15479/AT:ISTA:14926.","ama":"Hauschild R. Matlab script for analysis of clone dispersal. 2024. doi:10.15479/AT:ISTA:14926","ista":"Hauschild R. 2024. Matlab script for analysis of clone dispersal, ISTA, 10.15479/AT:ISTA:14926.","apa":"Hauschild, R. (2024). Matlab script for analysis of clone dispersal. ISTA. https://doi.org/10.15479/AT:ISTA:14926","ieee":"R. Hauschild, “Matlab script for analysis of clone dispersal.” ISTA, 2024."},"doi":"10.15479/AT:ISTA:14926","date_published":"2024-02-02T00:00:00Z","has_accepted_license":"1","month":"02","day":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14926","year":"2024","department":[{"_id":"Bio"}],"publisher":"ISTA","ddc":["570"],"title":"Matlab script for analysis of clone dispersal","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"15048"}]},"author":[{"full_name":"Hauschild, Robert","first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522"}],"file":[{"relation":"main_file","file_id":"14927","checksum":"df7f358ae19a176cf710c0a802ce31b1","success":1,"date_created":"2024-02-02T14:40:31Z","date_updated":"2024-02-02T14:40:31Z","access_level":"open_access","file_name":"README.md","content_type":"application/octet-stream","file_size":736,"creator":"rhauschild"},{"checksum":"10194cc11619eccd8f4b24472e465b7f","success":1,"date_updated":"2024-02-02T14:40:31Z","date_created":"2024-02-02T14:40:31Z","relation":"main_file","file_id":"14928","file_size":3543,"content_type":"application/x-zip-compressed","creator":"rhauschild","access_level":"open_access","file_name":"Supplementary_file_1.zip"}],"date_updated":"2024-03-04T07:28:25Z","date_created":"2024-02-02T14:42:26Z","type":"software","file_date_updated":"2024-02-02T14:40:31Z","license":"https://opensource.org/licenses/MIT"},{"scopus_import":"1","day":"23","article_processing_charge":"Yes","has_accepted_license":"1","article_type":"original","publication":"Science Advances","citation":{"ama":"Bao J, Stevens B, Kluft L, Muller CJ. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 2024;10(8). doi:10.1126/sciadv.adj6801","ista":"Bao J, Stevens B, Kluft L, Muller CJ. 2024. Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. 10(8), eadj6801.","apa":"Bao, J., Stevens, B., Kluft, L., & Muller, C. J. (2024). Intensification of daily tropical precipitation extremes from more organized convection. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adj6801","ieee":"J. Bao, B. Stevens, L. Kluft, and C. J. Muller, “Intensification of daily tropical precipitation extremes from more organized convection,” Science Advances, vol. 10, no. 8. American Association for the Advancement of Science, 2024.","mla":"Bao, Jiawei, et al. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances, vol. 10, no. 8, eadj6801, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adj6801.","short":"J. Bao, B. Stevens, L. Kluft, C.J. Muller, Science Advances 10 (2024).","chicago":"Bao, Jiawei, Bjorn Stevens, Lukas Kluft, and Caroline J Muller. “Intensification of Daily Tropical Precipitation Extremes from More Organized Convection.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adj6801."},"date_published":"2024-02-23T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Tropical precipitation extremes and their changes with surface warming are investigated using global storm resolving simulations and high-resolution observations. The simulations demonstrate that the mesoscale organization of convection, a process that cannot be physically represented by conventional global climate models, is important for the variations of tropical daily accumulated precipitation extremes. In both the simulations and observations, daily precipitation extremes increase in a more organized state, in association with larger, but less frequent, storms. Repeating the simulations for a warmer climate results in a robust increase in monthly-mean daily precipitation extremes. Higher precipitation percentiles have a greater sensitivity to convective organization, which is predicted to increase with warming. Without changes in organization, the strongest daily precipitation extremes over the tropical oceans increase at a rate close to Clausius-Clapeyron (CC) scaling. Thus, in a future warmer state with increased organization, the strongest daily precipitation extremes over oceans increase at a faster rate than CC scaling."}],"issue":"8","title":"Intensification of daily tropical precipitation extremes from more organized convection","status":"public","ddc":["550"],"intvolume":" 10","_id":"15047","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","file_name":"2024_ScienceAdv_Bao.pdf","file_size":800926,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"15051","checksum":"d4ec4f05a6d14745057e14d1b8bf45ae","success":1,"date_updated":"2024-03-04T07:34:00Z","date_created":"2024-03-04T07:34:00Z"}],"oa_version":"Published Version","month":"02","publication_identifier":{"eissn":["2375-2548"]},"quality_controlled":"1","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"},{"name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38394192"]},"language":[{"iso":"eng"}],"doi":"10.1126/sciadv.adj6801","article_number":"eadj6801","file_date_updated":"2024-03-04T07:34:00Z","ec_funded":1,"publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"CaMu"}],"acknowledgement":"This work is supported by the Max-Planck-Gesellschaft (MPG). We greatly appreciate computational resources from Deutsches Klimarechenzentrum (DKRZ) and the Jülich Supercomputing Centre (JSC). ICONA/O simulations are funded through the NextGEMS project by the EU’s Horizon 2020 programme (grant agreement no. 101003470). ICONA simulations are funded through the MONSOON-2.0 project (grant agreement no. 01LP1927A) which is supported from German Federal Ministry of Education and Research (BMBF). J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement no. 101034413). B.S. acknowledges funding from the EU’s Horizon 2020 programme (grant agreement no. 101003470). C.M. gratefully acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041).","year":"2024","pmid":1,"date_created":"2024-03-03T23:00:50Z","date_updated":"2024-03-05T09:26:47Z","volume":10,"author":[{"full_name":"Bao, Jiawei","first_name":"Jiawei","last_name":"Bao","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160"},{"full_name":"Stevens, Bjorn","last_name":"Stevens","first_name":"Bjorn"},{"full_name":"Kluft, Lukas","last_name":"Kluft","first_name":"Lukas"},{"first_name":"Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J"}],"related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/cloud-clustering-causes-more-extreme-rain/"}]}},{"day":"17","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","date_published":"2024-01-17T00:00:00Z","publication":"Neuron","citation":{"chicago":"Cheung, Giselle T, Florian Pauler, Peter Koppensteiner, Thomas Krausgruber, Carmen Streicher, Martin Schrammel, Natalie Y Özgen, et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron. Elsevier, 2024. https://doi.org/10.1016/j.neuron.2023.11.009.","short":"G.T. Cheung, F. Pauler, P. Koppensteiner, T. Krausgruber, C. Streicher, M. Schrammel, N.Y. Özgen, A. Ivec, C. Bock, R. Shigemoto, S. Hippenmeyer, Neuron 112 (2024) 230–246.e11.","mla":"Cheung, Giselle T., et al. “Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus.” Neuron, vol. 112, no. 2, Elsevier, 2024, p. 230–246.e11, doi:10.1016/j.neuron.2023.11.009.","apa":"Cheung, G. T., Pauler, F., Koppensteiner, P., Krausgruber, T., Streicher, C., Schrammel, M., … Hippenmeyer, S. (2024). Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.11.009","ieee":"G. T. Cheung et al., “Multipotent progenitors instruct ontogeny of the superior colliculus,” Neuron, vol. 112, no. 2. Elsevier, p. 230–246.e11, 2024.","ista":"Cheung GT, Pauler F, Koppensteiner P, Krausgruber T, Streicher C, Schrammel M, Özgen NY, Ivec A, Bock C, Shigemoto R, Hippenmeyer S. 2024. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 112(2), 230–246.e11.","ama":"Cheung GT, Pauler F, Koppensteiner P, et al. Multipotent progenitors instruct ontogeny of the superior colliculus. Neuron. 2024;112(2):230-246.e11. doi:10.1016/j.neuron.2023.11.009"},"article_type":"original","page":"230-246.e11","abstract":[{"lang":"eng","text":"The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration and is composed of a rich diversity of excitatory and inhibitory neurons and glia. However, the developmental principles directing the generation of SC cell-type diversity are not understood. Here, we pursued systematic cell lineage tracing in silico and in vivo, preserving full spatial information, using genetic mosaic analysis with double markers (MADM)-based clonal analysis with single-cell sequencing (MADM-CloneSeq). The analysis of clonally related cell lineages revealed that radial glial progenitors (RGPs) in SC are exceptionally multipotent. Individual resident RGPs have the capacity to produce all excitatory and inhibitory SC neuron types, even at the stage of terminal division. While individual clonal units show no pre-defined cellular composition, the establishment of appropriate relative proportions of distinct neuronal types occurs in a PTEN-dependent manner. Collectively, our findings provide an inaugural framework at the single-RGP/-cell level of the mammalian SC ontogeny."}],"issue":"2","type":"journal_article","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":5942467,"creator":"dernst","access_level":"open_access","file_name":"2024_Neuron_Cheung.pdf","checksum":"32b3788f7085cf44a84108d8faaff3ce","success":1,"date_created":"2024-02-06T13:56:15Z","date_updated":"2024-02-06T13:56:15Z","relation":"main_file","file_id":"14944"}],"_id":"12875","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Multipotent progenitors instruct ontogeny of the superior colliculus","ddc":["570"],"intvolume":" 112","month":"01","publication_identifier":{"issn":["0896-6273"]},"doi":"10.1016/j.neuron.2023.11.009","acknowledged_ssus":[{"_id":"Bio"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38096816"]},"quality_controlled":"1","project":[{"name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F07805"}],"file_date_updated":"2024-02-06T13:56:15Z","author":[{"last_name":"Cheung","first_name":"Giselle T","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T"},{"full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048"},{"full_name":"Koppensteiner, Peter","first_name":"Peter","last_name":"Koppensteiner","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3509-1948"},{"first_name":"Thomas","last_name":"Krausgruber","full_name":"Krausgruber, Thomas"},{"full_name":"Streicher, Carmen","last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schrammel","first_name":"Martin","id":"f13e7cae-e8bd-11ed-841a-96dedf69f46d","full_name":"Schrammel, Martin"},{"full_name":"Özgen, Natalie Y","last_name":"Özgen","first_name":"Natalie Y","id":"e68ece33-f6e0-11ea-865d-ae1031dcc090"},{"full_name":"Ivec, Alexis","id":"1d144691-e8be-11ed-9b33-bdd3077fad4c","first_name":"Alexis","last_name":"Ivec"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/the-pedigree-of-brain-cells/","relation":"press_release","description":"News on ISTA Website"}]},"date_created":"2023-04-27T09:41:48Z","date_updated":"2024-03-05T09:43:02Z","volume":112,"acknowledgement":"We thank Liqun Luo for his continued support, for providing essential resources for generating Fzd10-CreER mice which were generated in his laboratory, and for comments on the manuscript; W. Zhong for providing Nestin-Cre transgenic mouse line for this study; A. Heger for mouse colony management; R. Beattie and T. Asenov for designing and producing components of acute slice recovery chamber for MADM-CloneSeq experiments; and K. Leopold, J. Rodarte and N. Amberg for initial experiments, technical support and/or assistance. This study was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging & Optics Facility (IOF), Laboratory Support Facility (LSF), Miba Machine Shop, and Pre-clinical Facility (PCF). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional\r\nfunds; the Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H. ","year":"2024","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"SiHi"},{"_id":"RySh"}]},{"citation":{"ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology.","ieee":"J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” Nature Structural & Molecular Biology. Springer Nature, 2024.","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 2024. doi:10.1038/s41594-023-01201-6","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.","mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology, Springer Nature, 2024, doi:10.1038/s41594-023-01201-6.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology (2024)."},"publication":"Nature Structural & Molecular Biology","article_type":"original","date_published":"2024-02-05T00:00:00Z","keyword":["Molecular Biology","Structural Biology"],"article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"05","_id":"14979","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","status":"public","ddc":["570"],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38316877"]},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41594-023-01201-6","open_access":"1"}],"project":[{"call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1038/s41594-023-01201-6","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"month":"02","pmid":1,"year":"2024","acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","publisher":"Springer Nature","department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"publication_status":"epub_ahead","related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/"}]},"author":[{"full_name":"Datler, Julia","last_name":"Datler","first_name":"Julia","orcid":"0000-0002-3616-8580","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","first_name":"Jesse","last_name":"Hansen"},{"full_name":"Thader, Andreas","first_name":"Andreas","last_name":"Thader","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois"},{"last_name":"Bauer","first_name":"Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0","full_name":"Bauer, Lukas W"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"full_name":"Schur, Florian KM","last_name":"Schur","first_name":"Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-03-05T09:27:47Z","date_created":"2024-02-12T09:59:45Z"},{"date_published":"2024-01-09T00:00:00Z","article_type":"original","citation":{"mla":"Caballero Mancebo, Silvia, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics, Springer Nature, 2024, doi:10.1038/s41567-023-02302-1.","short":"S. Caballero Mancebo, R. Shinde, M. Bolger-Munro, M. Peruzzo, G. Szep, I. Steccari, D. Labrousse Arias, V. Zheden, J. Merrin, A. Callan-Jones, R. Voituriez, C.-P.J. Heisenberg, Nature Physics (2024).","chicago":"Caballero Mancebo, Silvia, Rushikesh Shinde, Madison Bolger-Munro, Matilda Peruzzo, Gregory Szep, Irene Steccari, David Labrousse Arias, et al. “Friction Forces Determine Cytoplasmic Reorganization and Shape Changes of Ascidian Oocytes upon Fertilization.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-023-02302-1.","ama":"Caballero Mancebo S, Shinde R, Bolger-Munro M, et al. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. 2024. doi:10.1038/s41567-023-02302-1","ista":"Caballero Mancebo S, Shinde R, Bolger-Munro M, Peruzzo M, Szep G, Steccari I, Labrousse Arias D, Zheden V, Merrin J, Callan-Jones A, Voituriez R, Heisenberg C-PJ. 2024. Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics.","ieee":"S. Caballero Mancebo et al., “Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization,” Nature Physics. Springer Nature, 2024.","apa":"Caballero Mancebo, S., Shinde, R., Bolger-Munro, M., Peruzzo, M., Szep, G., Steccari, I., … Heisenberg, C.-P. J. (2024). Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02302-1"},"publication":"Nature Physics","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"09","scopus_import":"1","oa_version":"Published Version","status":"public","title":"Friction forces determine cytoplasmic reorganization and shape changes of ascidian oocytes upon fertilization","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14846","abstract":[{"lang":"eng","text":"Contraction and flow of the actin cell cortex have emerged as a common principle by which cells reorganize their cytoplasm and take shape. However, how these cortical flows interact with adjacent cytoplasmic components, changing their form and localization, and how this affects cytoplasmic organization and cell shape remains unclear. Here we show that in ascidian oocytes, the cooperative activities of cortical actomyosin flows and deformation of the adjacent mitochondria-rich myoplasm drive oocyte cytoplasmic reorganization and shape changes following fertilization. We show that vegetal-directed cortical actomyosin flows, established upon oocyte fertilization, lead to both the accumulation of cortical actin at the vegetal pole of the zygote and compression and local buckling of the adjacent elastic solid-like myoplasm layer due to friction forces generated at their interface. Once cortical flows have ceased, the multiple myoplasm buckles resolve into one larger buckle, which again drives the formation of the contraction pole—a protuberance of the zygote’s vegetal pole where maternal mRNAs accumulate. Thus, our findings reveal a mechanism where cortical actomyosin network flows determine cytoplasmic reorganization and cell shape by deforming adjacent cytoplasmic components through friction forces."}],"type":"journal_article","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"NanoFab"}],"doi":"10.1038/s41567-023-02302-1","project":[{"name":"Control of embryonic cleavage pattern","call_identifier":"FWF","grant_number":"I03601","_id":"2646861A-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41567-023-02302-1"}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"month":"01","date_created":"2024-01-21T23:00:57Z","date_updated":"2024-03-05T09:33:38Z","related_material":{"link":[{"relation":"press_release","description":"News on ISTA Website","url":"https://ista.ac.at/en/news/stranger-than-friction-a-force-initiating-life/"}]},"author":[{"first_name":"Silvia","last_name":"Caballero Mancebo","id":"2F1E1758-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5223-3346","full_name":"Caballero Mancebo, Silvia"},{"last_name":"Shinde","first_name":"Rushikesh","full_name":"Shinde, Rushikesh"},{"id":"516F03FA-93A3-11EA-A7C5-D6BE3DDC885E","orcid":"0000-0002-8176-4824","first_name":"Madison","last_name":"Bolger-Munro","full_name":"Bolger-Munro, Madison"},{"full_name":"Peruzzo, Matilda","last_name":"Peruzzo","first_name":"Matilda","orcid":"0000-0002-3415-4628","id":"3F920B30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gregory","last_name":"Szep","id":"4BFB7762-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Gregory"},{"id":"2705C766-9FE2-11EA-B224-C6773DDC885E","last_name":"Steccari","first_name":"Irene","full_name":"Steccari, Irene"},{"full_name":"Labrousse Arias, David","last_name":"Labrousse Arias","first_name":"David","id":"CD573DF4-9ED3-11E9-9D77-3223E6697425"},{"full_name":"Zheden, Vanessa","first_name":"Vanessa","last_name":"Zheden","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9438-4783"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack"},{"full_name":"Callan-Jones, Andrew","first_name":"Andrew","last_name":"Callan-Jones"},{"first_name":"Raphaël","last_name":"Voituriez","full_name":"Voituriez, Raphaël"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"}],"publisher":"Springer Nature","department":[{"_id":"CaHe"},{"_id":"JoFi"},{"_id":"MiSi"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"publication_status":"epub_ahead","year":"2024","acknowledgement":"We would like to thank A. McDougall, E. Hannezo and the Heisenberg lab for fruitful discussions and reagents. We also thank E. Munro for the iMyo-YFP and Bra>iMyo-mScarlet constructs. This research was supported by the Scientific Service Units of the Institute of Science and Technology Austria through resources provided by the Electron Microscopy Facility, Imaging and Optics Facility and the Nanofabrication Facility. This work was supported by a Joint Project Grant from the FWF (I 3601-B27)."},{"title":"The genetic basis of a recent transition to live-bearing in marine snails","status":"public","intvolume":" 383","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14796","oa_version":"None","type":"journal_article","abstract":[{"lang":"eng","text":"Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step."}],"issue":"6678","article_type":"original","page":"114-119","publication":"Science","citation":{"mla":"Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982.","short":"S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119.","chicago":"Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982.","ama":"Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. Science. 2024;383(6678):114-119. doi:10.1126/science.adi2982","ista":"Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119.","apa":"Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adi2982","ieee":"S. Stankowski et al., “The genetic basis of a recent transition to live-bearing in marine snails,” Science, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024."},"date_published":"2024-01-05T00:00:00Z","scopus_import":"1","day":"05","article_processing_charge":"No","publication_status":"published","publisher":"American Association for the Advancement of Science","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"acknowledgement":"We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.).","year":"2024","pmid":1,"date_updated":"2024-03-05T09:35:25Z","date_created":"2024-01-14T23:00:56Z","volume":383,"author":[{"full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski"},{"first_name":"Zuzanna B.","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna B."},{"full_name":"Garlovsky, Martin D.","first_name":"Martin D.","last_name":"Garlovsky"},{"full_name":"Pal, Arka","last_name":"Pal","first_name":"Arka","orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425"},{"full_name":"Shipilina, Daria","first_name":"Daria","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226"},{"full_name":"Garcia Castillo, Diego Fernando","last_name":"Garcia Castillo","first_name":"Diego Fernando","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"},{"id":"d6ab5470-2fb3-11ed-8633-986a9b84edac","last_name":"Lifchitz","first_name":"Hila","full_name":"Lifchitz, Hila"},{"last_name":"Le Moan","first_name":"Alan","full_name":"Le Moan, Alan"},{"full_name":"Leder, Erica","first_name":"Erica","last_name":"Leder"},{"first_name":"James","last_name":"Reeve","full_name":"Reeve, James"},{"full_name":"Johannesson, Kerstin","first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","first_name":"Roger K.","last_name":"Butlin"}],"related_material":{"record":[{"status":"public","relation":"research_data","id":"14812"}],"link":[{"url":"https://ista.ac.at/en/news/the-snail-or-the-egg/","description":"News on ISTA Website","relation":"press_release"}]},"quality_controlled":"1","external_id":{"pmid":["38175895"]},"language":[{"iso":"eng"}],"doi":"10.1126/science.adi2982","month":"01","publication_identifier":{"eissn":["1095-9203"]}},{"day":"23","has_accepted_license":"1","article_processing_charge":"No","keyword":["Theoretical biology","Optimality","Evolution","Information"],"date_published":"2024-02-23T00:00:00Z","page":"158","citation":{"ama":"Hledik M. Genetic information and biological optimization. 2024. doi:10.15479/at:ista:15020","apa":"Hledik, M. (2024). Genetic information and biological optimization. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15020","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","mla":"Hledik, Michal. Genetic Information and Biological Optimization. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15020.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15020."},"abstract":[{"text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal.","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"date_updated":"2024-02-23T13:50:53Z","date_created":"2024-02-23T13:50:53Z","success":1,"checksum":"b2d3da47c98d481577a4baf68944fe41","file_id":"15021","relation":"main_file","creator":"mhledik","file_size":7102089,"content_type":"application/pdf","file_name":"hledik thesis pdfa 2b.pdf","access_level":"open_access"},{"file_id":"15022","relation":"source_file","date_updated":"2024-02-23T14:20:16Z","date_created":"2024-02-23T13:50:54Z","checksum":"eda9b9430da2610fee7ce1c1419a479a","file_name":"hledik thesis source.zip","access_level":"closed","creator":"mhledik","file_size":14014790,"content_type":"application/zip"}],"ddc":["576","519"],"title":"Genetic information and biological optimization","status":"public","_id":"15020","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"02","publication_identifier":{"issn":["2663 - 337X"]},"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:15020","project":[{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"grant_number":"101055327","_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes"}],"oa":1,"file_date_updated":"2024-02-23T14:20:16Z","ec_funded":1,"date_created":"2024-02-23T14:02:04Z","date_updated":"2024-03-06T14:22:52Z","author":[{"first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"7553"},{"relation":"part_of_dissertation","status":"public","id":"12081"},{"id":"7606","status":"public","relation":"part_of_dissertation"}]},"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Institute of Science and Technology Austria","year":"2024"},{"issue":"1","abstract":[{"lang":"eng","text":"Eva Benkova received a PhD in Biophysics at the Institute of Biophysics of the Czech Academy of Sciences in 1998. After working as a postdoc at the Max Planck Institute in Cologne and the Center for Plant Molecular Biology (ZMBP) in Tübingen, she became a group leader at the Plant Systems Biology Department of the Vlaams Instituut voor Biotechnologie (VIB) in Gent. In 2012, she transitioned to an Assistant Professor position at the Institute of Science and Technology Austria (ISTA) where she was later promoted to Professor. Since 2021, she has served as the Dean of the ISTA Graduate School. As a plant developmental biologist, she focuses on unraveling the molecular mechanisms and principles that underlie hormonal interactions in plants. In her current work, she explores the intricate connections between hormones and regulatory pathways that mediate the perception of environmental stimuli, including abiotic stress and nitrate availability."}],"type":"other_academic_publication","oa_version":"Published Version","intvolume":" 34","title":"Eva Benkova","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14842","article_processing_charge":"No","day":"08","date_published":"2024-01-08T00:00:00Z","page":"R3-R5","citation":{"ama":"Benková E. Eva Benkova. Vol 34. Elsevier; 2024:R3-R5. doi:10.1016/j.cub.2023.11.039","apa":"Benková, E. (2024). Eva Benkova. Current Biology (Vol. 34, pp. R3–R5). Elsevier. https://doi.org/10.1016/j.cub.2023.11.039","ieee":"E. Benková, Eva Benkova, vol. 34, no. 1. Elsevier, 2024, pp. R3–R5.","ista":"Benková E. 2024. Eva Benkova, Elsevier,p.","short":"E. Benková, Eva Benkova, Elsevier, 2024.","mla":"Benková, Eva. “Eva Benkova.” Current Biology, vol. 34, no. 1, Elsevier, 2024, pp. R3–5, doi:10.1016/j.cub.2023.11.039.","chicago":"Benková, Eva. Eva Benkova. Current Biology. Vol. 34. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.039."},"publication":"Current Biology","volume":34,"date_created":"2024-01-21T23:00:56Z","date_updated":"2024-03-12T12:19:12Z","author":[{"last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"department":[{"_id":"EvBe"}],"publisher":"Elsevier","publication_status":"published","year":"2024","publication_identifier":{"eissn":["1879-0445"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1016/j.cub.2023.11.039","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2023.11.039","open_access":"1"}]},{"day":"20","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","date_published":"2024-02-20T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","citation":{"mla":"Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences, vol. 121, no. 8, e2301449121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121.","short":"P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences 121 (2024).","chicago":"Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121.","ama":"Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 2024;121(8). doi:10.1073/pnas.2301449121","ista":"Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. 121(8), e2301449121.","apa":"Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121","ieee":"P. Koppensteiner et al., “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” Proceedings of the National Academy of Sciences, vol. 121, no. 8. Proceedings of the National Academy of Sciences, 2024."},"article_type":"original","abstract":[{"text":"GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n 2+\r\n -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.","lang":"eng"}],"issue":"8","type":"journal_article","oa_version":"Published Version","file":[{"file_size":13648221,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2024_PNAS_Koppensteiner.pdf","checksum":"b25b2a057c266ff317a48b0d54d6fc8a","success":1,"date_updated":"2024-03-12T13:42:42Z","date_created":"2024-03-12T13:42:42Z","relation":"main_file","file_id":"15110"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15084","ddc":["570"],"title":"GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles","status":"public","intvolume":" 121","month":"02","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"doi":"10.1073/pnas.2301449121","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["38346189"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"quality_controlled":"1","project":[{"grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2024-03-12T13:42:42Z","ec_funded":1,"article_number":"e2301449121","author":[{"full_name":"Koppensteiner, Peter","orcid":"0000-0002-3509-1948","id":"3B8B25A8-F248-11E8-B48F-1D18A9856A87","last_name":"Koppensteiner","first_name":"Peter"},{"first_name":"Pradeep","last_name":"Bhandari","id":"45EDD1BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0863-4481","full_name":"Bhandari, Pradeep"},{"first_name":"Hüseyin C","last_name":"Önal","id":"4659D740-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2771-2011","full_name":"Önal, Hüseyin C"},{"orcid":"0000-0003-0005-401X","id":"4305C450-F248-11E8-B48F-1D18A9856A87","last_name":"Borges Merjane","first_name":"Carolina","full_name":"Borges Merjane, Carolina"},{"id":"3B59276A-F248-11E8-B48F-1D18A9856A87","last_name":"Le Monnier","first_name":"Elodie","full_name":"Le Monnier, Elodie"},{"full_name":"Roy, Utsa","first_name":"Utsa","last_name":"Roy","id":"4d26cf11-5355-11ee-ae5a-eb05e255b9b2"},{"last_name":"Nakamura","first_name":"Yukihiro","full_name":"Nakamura, Yukihiro"},{"full_name":"Sadakata, Tetsushi","first_name":"Tetsushi","last_name":"Sadakata"},{"full_name":"Sanbo, Makoto","first_name":"Makoto","last_name":"Sanbo"},{"full_name":"Hirabayashi, Masumi","first_name":"Masumi","last_name":"Hirabayashi"},{"full_name":"Rhee, JeongSeop","last_name":"Rhee","first_name":"JeongSeop"},{"last_name":"Brose","first_name":"Nils","full_name":"Brose, Nils"},{"full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/","relation":"press_release","description":"News on ISTA Website"}],"record":[{"status":"public","relation":"research_data","id":"13173"}]},"date_created":"2024-03-05T09:23:55Z","date_updated":"2024-03-12T13:44:18Z","volume":121,"acknowledgement":"We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support.","year":"2024","pmid":1,"publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"RySh"},{"_id":"PeJo"}]},{"_id":"15083","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 121","ddc":["000"],"status":"public","title":"Efficiency and resilience of cooperation in asymmetric social dilemmas","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2024_PNAS_Huebner.pdf","creator":"dernst","content_type":"application/pdf","file_size":2203220,"file_id":"15109","relation":"main_file","success":1,"checksum":"068520e3efd4d008bb9177e8aedb7d22","date_created":"2024-03-12T13:12:22Z","date_updated":"2024-03-12T13:12:22Z"}],"type":"journal_article","issue":"10","abstract":[{"text":"Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation.","lang":"eng"}],"citation":{"ista":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 121(10), e2315558121.","ieee":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency and resilience of cooperation in asymmetric social dilemmas,” Proceedings of the National Academy of Sciences, vol. 121, no. 10. Proceedings of the National Academy of Sciences, 2024.","apa":"Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., & Kleshnina, M. (2024). Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2315558121","ama":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences. 2024;121(10). doi:10.1073/pnas.2315558121","chicago":"Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2315558121.","mla":"Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Proceedings of the National Academy of Sciences, vol. 121, no. 10, e2315558121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2315558121.","short":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of the National Academy of Sciences 121 (2024)."},"publication":"Proceedings of the National Academy of Sciences","article_type":"original","date_published":"2024-03-05T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","day":"05","pmid":1,"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010) (to M.K.).","year":"2024","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"KrCh"}],"publication_status":"published","related_material":{"record":[{"id":"15108","status":"public","relation":"research_data"}],"link":[{"url":"https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/","description":"News on ISTA Website","relation":"press_release"}]},"author":[{"full_name":"Hübner, Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","first_name":"Valentin","last_name":"Hübner"},{"first_name":"Manuel","last_name":"Staab","full_name":"Staab, Manuel"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"full_name":"Kleshnina, Maria","last_name":"Kleshnina","first_name":"Maria"}],"volume":121,"date_created":"2024-03-05T09:18:49Z","date_updated":"2024-03-12T13:29:25Z","article_number":"e2315558121","ec_funded":1,"file_date_updated":"2024-03-12T13:12:22Z","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"pmid":["38408249"]},"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"quality_controlled":"1","doi":"10.1073/pnas.2315558121","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"03"},{"oa_version":"Published Version","date_updated":"2024-03-12T13:29:26Z","date_created":"2024-03-12T13:02:58Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"15083"}]},"author":[{"full_name":"Hübner, Valentin","last_name":"Hübner","first_name":"Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910"},{"full_name":"Kleshnina, Maria","first_name":"Maria","last_name":"Kleshnina"}],"department":[{"_id":"KrCh"}],"publisher":"Zenodo","title":"Computer code for \"Efficiency and resilience of cooperation in asymmetric social dilemmas\"","status":"public","ddc":["000"],"year":"2024","_id":"15108","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"in the research article \"Efficiency and resilience of cooperation in asymmetric social dilemmas\" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina).\r\n\r\nWe used different implementations for the case of two and three players, both described below.","lang":"eng"}],"type":"research_data_reference","doi":"10.5281/ZENODO.10639167","date_published":"2024-02-09T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://10.5281/zenodo.10639167"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ama":"Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” 2024. doi:10.5281/ZENODO.10639167","ista":"Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas’, Zenodo, 10.5281/ZENODO.10639167.","apa":"Hübner, V., & Kleshnina, M. (2024). Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” Zenodo. https://doi.org/10.5281/ZENODO.10639167","ieee":"V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas.’” Zenodo, 2024.","mla":"Hübner, Valentin, and Maria Kleshnina. Computer Code for “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Zenodo, 2024, doi:10.5281/ZENODO.10639167.","short":"V. Hübner, M. Kleshnina, (2024).","chicago":"Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10639167."},"oa":1,"has_accepted_license":"1","article_processing_charge":"No","day":"09","month":"02"},{"author":[{"last_name":"Schmidt","first_name":"Hauke","full_name":"Schmidt, Hauke"},{"full_name":"Rast, Sebastian","first_name":"Sebastian","last_name":"Rast"},{"id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","last_name":"Bao","first_name":"Jiawei","full_name":"Bao, Jiawei"},{"last_name":"Cassim","first_name":"Amrit","full_name":"Cassim, Amrit"},{"full_name":"Fang, Shih Wei","last_name":"Fang","first_name":"Shih Wei"},{"first_name":"Diego","last_name":"Jimenez-De La Cuesta","full_name":"Jimenez-De La Cuesta, Diego"},{"first_name":"Paul","last_name":"Keil","full_name":"Keil, Paul"},{"full_name":"Kluft, Lukas","first_name":"Lukas","last_name":"Kluft"},{"first_name":"Clarissa","last_name":"Kroll","full_name":"Kroll, Clarissa"},{"full_name":"Lang, Theresa","first_name":"Theresa","last_name":"Lang"},{"last_name":"Niemeier","first_name":"Ulrike","full_name":"Niemeier, Ulrike"},{"full_name":"Schneidereit, Andrea","first_name":"Andrea","last_name":"Schneidereit"},{"first_name":"Andrew I.L.","last_name":"Williams","full_name":"Williams, Andrew I.L."},{"full_name":"Stevens, Bjorn","first_name":"Bjorn","last_name":"Stevens"}],"volume":17,"date_created":"2024-03-10T23:00:53Z","date_updated":"2024-03-13T09:01:20Z","acknowledgement":"The authors wish to thank Ann Kristin Naumann and three anonymous reviewers for very helpful comments on an earlier version of this paper. We are grateful to René Redler and Karl-Hermann Wieners for useful recommendations regarding running the simulations. We thank Luis Kornblueh for providing an external vertical grid generator and resolving the memory requirements for the very fine vertical grids. We acknowledge Hauke Schulz for providing the radiosonde data. The simulations were run at the German Climate Computing Center (DKRZ), and we thank the DKRZ staff for their support.\r\nHauke Schmidt and Diego Jimenez-de la Cuesta received financial support from the SOCTOC project within the framework of the ROMIC program, funded by the German Ministry of Education and Research (BMBF) (grant no. 01LG1903A).\r\nThe article processing charges for this open-access publication were covered by the Max Planck Society.","year":"2024","department":[{"_id":"CaMu"}],"publisher":"European Geosciences Union","publication_status":"published","file_date_updated":"2024-03-13T08:59:21Z","doi":"10.5194/gmd-17-1563-2024","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","publication_identifier":{"eissn":["1991-9603"],"issn":["1991-959X"]},"month":"02","file":[{"creator":"dernst","file_size":13364601,"content_type":"application/pdf","access_level":"open_access","file_name":"2024_GeoscientificModelDev_Schmidt.pdf","success":1,"checksum":"270d2340402729b0532f7072ea914cae","date_created":"2024-03-13T08:59:21Z","date_updated":"2024-03-13T08:59:21Z","file_id":"15111","relation":"main_file"}],"oa_version":"Published Version","_id":"15097","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 17","title":"Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model","ddc":["550"],"status":"public","issue":"4","abstract":[{"text":"Global storm-resolving models (GSRMs) use strongly refined horizontal grids compared with the climate models typically used in the Coupled Model Intercomparison Project (CMIP) but employ comparable vertical grid spacings. Here, we study how changes in the vertical grid spacing and adjustments to the integration time step affect the basic climate quantities simulated by the ICON-Sapphire atmospheric GSRM. Simulations are performed over a 45 d period for five different vertical grids with between 55 and 540 vertical layers and maximum tropospheric vertical grid spacings of between 800 and 50 m, respectively. The effects of changes in the vertical grid spacing are compared with the effects of reducing the horizontal grid spacing from 5 to 2.5 km. For most of the quantities considered, halving the vertical grid spacing has a smaller effect than halving the horizontal grid spacing, but it is not negligible. Each halving of the vertical grid spacing, along with the necessary reductions in time step length, increases cloud liquid water by about 7 %, compared with an approximate 16 % decrease for halving the horizontal grid spacing. The effect is due to both the vertical grid refinement and the time step reduction. There is no tendency toward convergence in the range of grid spacings tested here. The cloud ice amount also increases with a refinement in the vertical grid, but it is hardly affected by the time step length and does show a tendency to converge. While the effect on shortwave radiation is globally dominated by the altered reflection due to the change in the cloud liquid water content, the effect on longwave radiation is more difficult to interpret because changes in the cloud ice concentration and cloud fraction are anticorrelated in some regions. The simulations show that using a maximum tropospheric vertical grid spacing larger than 400 m would increase the truncation error strongly. Computing time investments in a further vertical grid refinement can affect the truncation errors of GSRMs similarly to comparable investments in horizontal refinement, because halving the vertical grid spacing is generally cheaper than halving the horizontal grid spacing. However, convergence of boundary layer cloud properties cannot be expected, even for the smallest maximum tropospheric grid spacing of 50 m used in this study.","lang":"eng"}],"type":"journal_article","date_published":"2024-02-22T00:00:00Z","citation":{"ama":"Schmidt H, Rast S, Bao J, et al. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 2024;17(4):1563-1584. doi:10.5194/gmd-17-1563-2024","ista":"Schmidt H, Rast S, Bao J, Cassim A, Fang SW, Jimenez-De La Cuesta D, Keil P, Kluft L, Kroll C, Lang T, Niemeier U, Schneidereit A, Williams AIL, Stevens B. 2024. Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. 17(4), 1563–1584.","ieee":"H. Schmidt et al., “Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model,” Geoscientific Model Development, vol. 17, no. 4. European Geosciences Union, pp. 1563–1584, 2024.","apa":"Schmidt, H., Rast, S., Bao, J., Cassim, A., Fang, S. W., Jimenez-De La Cuesta, D., … Stevens, B. (2024). Effects of vertical grid spacing on the climate simulated in the ICON-Sapphire global storm-resolving model. Geoscientific Model Development. European Geosciences Union. https://doi.org/10.5194/gmd-17-1563-2024","mla":"Schmidt, Hauke, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development, vol. 17, no. 4, European Geosciences Union, 2024, pp. 1563–84, doi:10.5194/gmd-17-1563-2024.","short":"H. Schmidt, S. Rast, J. Bao, A. Cassim, S.W. Fang, D. Jimenez-De La Cuesta, P. Keil, L. Kluft, C. Kroll, T. Lang, U. Niemeier, A. Schneidereit, A.I.L. Williams, B. Stevens, Geoscientific Model Development 17 (2024) 1563–1584.","chicago":"Schmidt, Hauke, Sebastian Rast, Jiawei Bao, Amrit Cassim, Shih Wei Fang, Diego Jimenez-De La Cuesta, Paul Keil, et al. “Effects of Vertical Grid Spacing on the Climate Simulated in the ICON-Sapphire Global Storm-Resolving Model.” Geoscientific Model Development. European Geosciences Union, 2024. https://doi.org/10.5194/gmd-17-1563-2024."},"publication":"Geoscientific Model Development","page":"1563-1584","article_type":"original","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"22","scopus_import":"1"},{"day":"26","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","scopus_import":"1","keyword":["Elliptic curves","Néron models","division polynomials","height functions","discrete valuation rings"],"date_published":"2024-02-26T00:00:00Z","publication":"Proceedings of the Royal Society of Edinburgh Section A: Mathematics","citation":{"chicago":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024. https://doi.org/10.1017/prm.2024.7.","mla":"Naskręcki, Bartosz, and Matteo Verzobio. “Common Valuations of Division Polynomials.” Proceedings of the Royal Society of Edinburgh Section A: Mathematics, 2203.02015, Cambridge University Press, 2024, doi:10.1017/prm.2024.7.","short":"B. Naskręcki, M. Verzobio, Proceedings of the Royal Society of Edinburgh Section A: Mathematics (2024).","ista":"Naskręcki B, Verzobio M. 2024. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics., 2203.02015.","ieee":"B. Naskręcki and M. Verzobio, “Common valuations of division polynomials,” Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press, 2024.","apa":"Naskręcki, B., & Verzobio, M. (2024). Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. Cambridge University Press. https://doi.org/10.1017/prm.2024.7","ama":"Naskręcki B, Verzobio M. Common valuations of division polynomials. Proceedings of the Royal Society of Edinburgh Section A: Mathematics. 2024. doi:10.1017/prm.2024.7"},"article_type":"original","abstract":[{"lang":"eng","text":"In this note, we prove a formula for the cancellation exponent kv,n between division polynomials ψn and ϕn associated with a sequence {nP}n∈N of points on an elliptic curve E defined over a discrete valuation field K. The formula greatly generalizes the previously known special cases and treats also the case of non-standard Kodaira types for non-perfect residue fields."}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12311","ddc":["510"],"title":"Common valuations of division polynomials","status":"public","month":"02","publication_identifier":{"issn":["0308-2105"],"eissn":["1473-7124"]},"doi":"10.1017/prm.2024.7","language":[{"iso":"eng"}],"external_id":{"arxiv":["2203.02015"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1017/prm.2024.7"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"ec_funded":1,"article_number":"2203.02015","author":[{"last_name":"Naskręcki","first_name":"Bartosz","full_name":"Naskręcki, Bartosz"},{"id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","orcid":"0000-0002-0854-0306","first_name":"Matteo","last_name":"Verzobio","full_name":"Verzobio, Matteo"}],"date_created":"2023-01-16T11:45:22Z","date_updated":"2024-03-13T11:55:21Z","acknowledgement":"Silverman, and Paul Voutier for the comments on the earlier version of this paper. The first author acknowledges the support by Dioscuri programme initiated by the Max Planck Society, jointly managed with the National Science Centre (Poland), and mutually funded by the Polish Ministry of Science and Higher Education and the German Federal Ministry of Education and Research. The second author has been supported by MIUR (Italy) through PRIN 2017 ‘Geometric, algebraic and analytic methods in arithmetic’ and has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","year":"2024","publication_status":"epub_ahead","publisher":"Cambridge University Press","department":[{"_id":"TiBr"}]},{"external_id":{"pmid":["38395682"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"main_file_link":[{"url":"https://doi.org/10.1016/j.tig.2024.01.002","open_access":"1"}],"quality_controlled":"1","doi":"10.1016/j.tig.2024.01.002","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0168-9525"],"eissn":["1362-4555"]},"month":"02","pmid":1,"year":"2024","acknowledgement":"KJ, MR, and RKB were supported by grants from the Swedish Research Council (2021-0419, 2021-05243, and 2018-03695, respectively). RKB was also supported by the Leverhulme Trust (RPG-2021-141), RF by FCT- Portuguese Science Foundation (PTDC/BIA-EVL/1614/2021 and 2020.00275.CEECIND), and AMW by Norwegian Research Council RCN (Project number 315287). We thank the members of the Integration of Speciation Research network for stimulating discussions, the Littorina research community for important contributions of data and analyses, and Cynthia Riginos for useful comments on an earlier draft.","department":[{"_id":"NiBa"}],"publisher":"Cell Press","publication_status":"epub_ahead","author":[{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"last_name":"Faria","first_name":"Rui","full_name":"Faria, Rui"},{"last_name":"Le Moan","first_name":"Alan","full_name":"Le Moan, Alan"},{"last_name":"Rafajlović","first_name":"Marina","full_name":"Rafajlović, Marina"},{"id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969","first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M"},{"full_name":"Butlin, Roger K.","last_name":"Butlin","first_name":"Roger K."},{"id":"43161670-5719-11EA-8025-FABC3DDC885E","first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean"}],"date_updated":"2024-03-13T12:08:57Z","date_created":"2024-03-10T23:00:54Z","citation":{"apa":"Johannesson, K., Faria, R., Le Moan, A., Rafajlović, M., Westram, A. M., Butlin, R. K., & Stankowski, S. (2024). Diverse pathways to speciation revealed by marine snails. Trends in Genetics. Cell Press. https://doi.org/10.1016/j.tig.2024.01.002","ieee":"K. Johannesson et al., “Diverse pathways to speciation revealed by marine snails,” Trends in Genetics. Cell Press, 2024.","ista":"Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. 2024. Diverse pathways to speciation revealed by marine snails. Trends in Genetics.","ama":"Johannesson K, Faria R, Le Moan A, et al. Diverse pathways to speciation revealed by marine snails. Trends in Genetics. 2024. doi:10.1016/j.tig.2024.01.002","chicago":"Johannesson, Kerstin, Rui Faria, Alan Le Moan, Marina Rafajlović, Anja M Westram, Roger K. Butlin, and Sean Stankowski. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics. Cell Press, 2024. https://doi.org/10.1016/j.tig.2024.01.002.","short":"K. Johannesson, R. Faria, A. Le Moan, M. Rafajlović, A.M. Westram, R.K. Butlin, S. Stankowski, Trends in Genetics (2024).","mla":"Johannesson, Kerstin, et al. “Diverse Pathways to Speciation Revealed by Marine Snails.” Trends in Genetics, Cell Press, 2024, doi:10.1016/j.tig.2024.01.002."},"publication":"Trends in Genetics","article_type":"review","date_published":"2024-02-22T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15099","ddc":["570"],"title":"Diverse pathways to speciation revealed by marine snails","status":"public","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems."}]},{"month":"02","publication_identifier":{"eissn":["1432-1807"],"issn":["0025-5831"]},"language":[{"iso":"eng"}],"doi":"10.1007/s00208-024-02812-0","quality_controlled":"1","project":[{"name":"Bridging Scales in Random Materials","call_identifier":"H2020","grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1007/s00208-024-02812-0"}],"oa":1,"external_id":{"arxiv":["2306.11081"]},"ec_funded":1,"date_updated":"2024-03-13T12:20:23Z","date_created":"2024-03-10T23:00:54Z","author":[{"full_name":"Agresti, Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","first_name":"Antonio","last_name":"Agresti"},{"full_name":"Luongo, Eliseo","first_name":"Eliseo","last_name":"Luongo"}],"publication_status":"epub_ahead","department":[{"_id":"JuFi"}],"publisher":"Springer Nature","acknowledgement":"The authors thank Professor Franco Flandoli for useful discussions and valuable insight into the subject. In particular, A.A. would like to thank professor Franco Flandoli for hosting and financially contributing to his research visit at Scuola Normale di Pisa in January 2023, where this work started. E.L. would like to express sincere gratitude to Professor Marco Fuhrman for igniting his interest in this particular field of research. E.L. want to thank Professor Matthias Hieber and Dr. Martin Saal for useful discussions. Finally, the authors thank the anonymous referee for helpful comments which improved the paper from its initial version.Open access funding provided by Scuola Normale Superiore within the CRUI-CARE Agreement. A. Agresti has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 948819).","year":"2024","day":"27","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2024-02-27T00:00:00Z","article_type":"original","publication":"Mathematische Annalen","citation":{"ama":"Agresti A, Luongo E. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. 2024. doi:10.1007/s00208-024-02812-0","ista":"Agresti A, Luongo E. 2024. Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen.","ieee":"A. Agresti and E. Luongo, “Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions,” Mathematische Annalen. Springer Nature, 2024.","apa":"Agresti, A., & Luongo, E. (2024). Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions. Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-024-02812-0","mla":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen, Springer Nature, 2024, doi:10.1007/s00208-024-02812-0.","short":"A. Agresti, E. Luongo, Mathematische Annalen (2024).","chicago":"Agresti, Antonio, and Eliseo Luongo. “Global Well-Posedness and Interior Regularity of 2D Navier-Stokes Equations with Stochastic Boundary Conditions.” Mathematische Annalen. Springer Nature, 2024. https://doi.org/10.1007/s00208-024-02812-0."},"abstract":[{"text":"The paper is devoted to the analysis of the global well-posedness and the interior regularity of the 2D Navier–Stokes equations with inhomogeneous stochastic boundary conditions. The noise, white in time and coloured in space, can be interpreted as the physical law describing the driving mechanism on the atmosphere–ocean interface, i.e. as a balance of the shear stress of the ocean and the horizontal wind force.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","title":"Global well-posedness and interior regularity of 2D Navier-Stokes equations with stochastic boundary conditions","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15098"},{"ec_funded":1,"publication_status":"inpress","department":[{"_id":"PeJo"},{"_id":"EM-Fac"},{"_id":"RySh"}],"publisher":"Elsevier","year":"2024","acknowledgement":"We thank Drs. David DiGregorio and Erwin Neher for critically reading an earlier version of the manuscript, Ralf Schneggenburger for helpful discussions, Benjamin Suter and Katharina Lichter for support with image analysis, Chris Wojtan for advice on numerical solution of partial differential equations, Maria Reva for help with Ripley analysis, Alois Schlögl for programming, and Akari Hagiwara and Toshihisa Ohtsuka for anti-ELKS antibody. We are grateful to Florian Marr, Christina Altmutter, and Vanessa Zheden for excellent technical assistance and to Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA (Electron Microscopy Facility, Preclinical Facility, and Machine Shop). The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 692692), the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein award; P 36232-B), all to P.J., and a DOC fellowship of the Austrian Academy of Sciences to J.-J.C.","pmid":1,"date_updated":"2024-03-14T13:14:18Z","date_created":"2024-01-21T23:00:56Z","author":[{"last_name":"Chen","first_name":"JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, JingJing"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","last_name":"Kaufmann","first_name":"Walter"},{"full_name":"Chen, Chong","last_name":"Chen","first_name":"Chong","id":"3DFD581A-F248-11E8-B48F-1D18A9856A87"},{"id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Itaru","last_name":"Arai","full_name":"Arai, Itaru"},{"full_name":"Kim, Olena","id":"3F8ABDDA-F248-11E8-B48F-1D18A9856A87","first_name":"Olena","last_name":"Kim"},{"first_name":"Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas"}],"related_material":{"link":[{"description":"News on ISTA Website","relation":"press_release","url":"https://ista.ac.at/en/news/synapses-brought-to-the-point/"}],"record":[{"status":"public","relation":"dissertation_contains","id":"15101"}]},"month":"01","publication_identifier":{"eissn":["1097-4199"],"issn":["0896-6273"]},"quality_controlled":"1","project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits"},{"grant_number":"25383","_id":"26B66A3E-B435-11E9-9278-68D0E5697425","name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse"}],"external_id":{"pmid":["38215739"]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"PreCl"},{"_id":"M-Shop"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.neuron.2023.12.002","type":"journal_article","abstract":[{"text":"The coupling between Ca2+ channels and release sensors is a key factor defining the signaling properties of a synapse. However, the coupling nanotopography at many synapses remains unknown, and it is unclear how it changes during development. To address these questions, we examined coupling at the cerebellar inhibitory basket cell (BC)-Purkinje cell (PC) synapse. Biophysical analysis of transmission by paired recording and intracellular pipette perfusion revealed that the effects of exogenous Ca2+ chelators decreased during development, despite constant reliance of release on P/Q-type Ca2+ channels. Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters throughout development, whereas docked vesicles were only clustered at later developmental stages. Modeling suggested a developmental transformation from a more random to a more clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic transmission.","lang":"eng"}],"title":"Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse","status":"public","_id":"14843","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","scopus_import":"1","day":"11","article_processing_charge":"No","article_type":"original","publication":"Neuron","citation":{"chicago":"Chen, JingJing, Walter Kaufmann, Chong Chen, itaru Arai, Olena Kim, Ryuichi Shigemoto, and Peter M Jonas. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron. Elsevier, n.d. https://doi.org/10.1016/j.neuron.2023.12.002.","mla":"Chen, JingJing, et al. “Developmental Transformation of Ca2+ Channel-Vesicle Nanotopography at a Central GABAergic Synapse.” Neuron, Elsevier, doi:10.1016/j.neuron.2023.12.002.","short":"J. Chen, W. Kaufmann, C. Chen, itaru Arai, O. Kim, R. Shigemoto, P.M. Jonas, Neuron (n.d.).","ista":"Chen J, Kaufmann W, Chen C, Arai itaru, Kim O, Shigemoto R, Jonas PM. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron.","ieee":"J. Chen et al., “Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse,” Neuron. Elsevier.","apa":"Chen, J., Kaufmann, W., Chen, C., Arai, itaru, Kim, O., Shigemoto, R., & Jonas, P. M. (n.d.). Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2023.12.002","ama":"Chen J, Kaufmann W, Chen C, et al. Developmental transformation of Ca2+ channel-vesicle nanotopography at a central GABAergic synapse. Neuron. doi:10.1016/j.neuron.2023.12.002"},"date_published":"2024-01-11T00:00:00Z"},{"day":"11","has_accepted_license":"1","article_processing_charge":"No","date_published":"2024-03-11T00:00:00Z","citation":{"short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","mla":"Chen, JingJing. Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15101.","chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15101.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","apa":"Chen, J. (2024). Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15101","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria."},"page":"84","type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"creator":"jchen","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":11271363,"file_name":"Thesis_Jingjing CHEN.docx","access_level":"closed","date_updated":"2024-03-12T07:12:17Z","date_created":"2024-03-11T14:10:58Z","checksum":"db4947474ffa271e66c254b6fe876a55","file_id":"15104","relation":"source_file"},{"date_updated":"2024-03-11T14:11:06Z","date_created":"2024-03-11T14:11:06Z","checksum":"a5eeae8b5702cd540f5d03469bc33dde","relation":"main_file","embargo":"2024-04-01","file_id":"15105","content_type":"application/pdf","file_size":16627311,"creator":"jchen","embargo_to":"open_access","file_name":"Thesis_Jingjing CHEN_merged.pdf","access_level":"closed"}],"oa_version":"Published Version","_id":"15101","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","ddc":["570"],"month":"03","publication_identifier":{"issn":["2663 - 337X"]},"doi":"10.15479/at:ista:15101","degree_awarded":"PhD","supervisor":[{"last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Mechanisms of GABA release in hippocampal circuits","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","_id":"26B66A3E-B435-11E9-9278-68D0E5697425","grant_number":"25383"}],"file_date_updated":"2024-03-12T07:12:17Z","ec_funded":1,"author":[{"full_name":"Chen, JingJing","first_name":"JingJing","last_name":"Chen","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"14843"}]},"date_updated":"2024-03-14T13:14:19Z","date_created":"2024-03-11T10:09:54Z","year":"2024","publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"PeJo"}]},{"abstract":[{"lang":"eng","text":"Quantum computers are increasing in size and quality but are still very noisy. Error mitigation extends the size of the quantum circuits that noisy devices can meaningfully execute. However, state-of-the-art error mitigation methods are hard to implement and the limited qubit connectivity in superconducting qubit devices restricts most applications to the hardware's native topology. Here we show a quantum approximate optimization algorithm (QAOA) on nonplanar random regular graphs with up to 40 nodes enabled by a machine learning-based error mitigation. We use a swap network with careful decision-variable-to-qubit mapping and a feed-forward neural network to optimize a depth-two QAOA on up to 40 qubits. We observe a meaningful parameter optimization for the largest graph which requires running quantum circuits with 958 two-qubit gates. Our paper emphasizes the need to mitigate samples, and not only expectation values, in quantum approximate optimization. These results are a step towards executing quantum approximate optimization at a scale that is not classically simulable. Reaching such system sizes is key to properly understanding the true potential of heuristic algorithms like QAOA."}],"issue":"1","type":"journal_article","oa_version":"Published Version","file":[{"date_created":"2024-03-19T07:16:38Z","date_updated":"2024-03-19T07:16:38Z","checksum":"274c9f1b15b3547a10a03f39e4ccc582","success":1,"relation":"main_file","file_id":"15123","content_type":"application/pdf","file_size":2777593,"creator":"dernst","file_name":"2024_PhysicalReviewResearch_Sack.pdf","access_level":"open_access"}],"_id":"15122","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation","ddc":["530"],"intvolume":" 6","day":"01","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2024-03-01T00:00:00Z","publication":"Physical Review Research","citation":{"mla":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review Research, vol. 6, no. 1, 013223, American Physical Society, 2024, doi:10.1103/PhysRevResearch.6.013223.","short":"S. Sack, D.J. Egger, Physical Review Research 6 (2024).","chicago":"Sack, Stefan, and Daniel J. Egger. “Large-Scale Quantum Approximate Optimization on Nonplanar Graphs with Machine Learning Noise Mitigation.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/PhysRevResearch.6.013223.","ama":"Sack S, Egger DJ. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 2024;6(1). doi:10.1103/PhysRevResearch.6.013223","ista":"Sack S, Egger DJ. 2024. Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. 6(1), 013223.","apa":"Sack, S., & Egger, D. J. (2024). Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.6.013223","ieee":"S. Sack and D. J. Egger, “Large-scale quantum approximate optimization on nonplanar graphs with machine learning noise mitigation,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024."},"article_type":"original","file_date_updated":"2024-03-19T07:16:38Z","article_number":"013223","author":[{"full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","orcid":"0000-0001-5400-8508","first_name":"Stefan","last_name":"Sack"},{"first_name":"Daniel J.","last_name":"Egger","full_name":"Egger, Daniel J."}],"date_created":"2024-03-17T23:00:59Z","date_updated":"2024-03-19T07:24:03Z","volume":6,"acknowledgement":"S.H.S. acknowledges support from the IBM Ph.D. fellowship 2022 in quantum computing. The authors also thank M. Serbyn, R. Kueng, R. A. Medina, and S. Woerner for fruitful discussions.","year":"2024","publication_status":"published","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","month":"03","publication_identifier":{"issn":["2643-1564"]},"doi":"10.1103/PhysRevResearch.6.013223","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2307.14427"]},"oa":1,"quality_controlled":"1","project":[{"name":"Quantum_Quantum Circuits and Software_Variational quantum algorithms on NISQ devices","_id":"bd660c93-d553-11ed-ba76-fb0fb6f49c0d"}]},{"publication_identifier":{"eissn":["2058-5276"]},"month":"03","external_id":{"pmid":["38443575"]},"project":[{"name":"Understanding bacterial cell division by in vitro\r\nreconstitution","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"}],"quality_controlled":"1","doi":"10.1038/s41564-024-01600-5","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"}],"pmid":1,"year":"2024","acknowledgement":"We thank X. Ye (ISTA) for providing the His–SUMO expression plasmid pSVA13429. pCDB302 was a gift from C. Bahl (Addgene plasmid number 113673; http://n2t.net/addgene:113673; RRID Addgene_113673). We thank B. Ahsan, G. Sharov, G. Cannone and S. Chen from the Medical Research Council (MRC) LMB Electron Microscopy Facility for help and support. We thank Scientific Computing at the MRC LMB for their support. We thank L. Trübestein and N. Krasnici of the protein service unit of the ISTA Lab Support Facility for help with the SEC coupled with multi-angle light scattering experiments. We thank D. Grohmann and R. Reichelt from the Archaea Centre at the University of Regensburg for providing the P. furiosus cell material. P.N. and S.-V.A. were supported by a Momentum grant from the Volkswagen (VW) Foundation (grant number 94933). D.K.-C. and D.B. were supported by the VW Stiftung ‘Life?’ programme (to J.L.; grant number Az 96727) and by the MRC, as part of UK Research and Innovation (UKRI), MRC file reference number U105184326 (to J.L.). N.T. and S.G. acknowledge support from the French Government’s Investissement d’Avenir program, Laboratoire d’Excellence ‘Integrative Biology of Emerging Infectious Diseases’ (grant number ANR-10-LABX-62-IBEID), and the computational and storage services (Maestro cluster) provided by the IT department at Institut Pasteur. M.K. and M.L. were supported by the Austrian Science Fund (FWF) Stand-Alone P34607. For the purpose of open access, the MRC Laboratory of Molecular Biology has applied a CC BY public copyright licence to any author accepted manuscript version arising.","publisher":"Springer Nature","department":[{"_id":"MaLo"}],"publication_status":"published","author":[{"full_name":"Nußbaum, Phillip","first_name":"Phillip","last_name":"Nußbaum"},{"first_name":"Danguole","last_name":"Kureisaite-Ciziene","full_name":"Kureisaite-Ciziene, Danguole"},{"full_name":"Bellini, Dom","first_name":"Dom","last_name":"Bellini"},{"full_name":"Van Der Does, Chris","last_name":"Van Der Does","first_name":"Chris"},{"full_name":"Kojic, Marko","last_name":"Kojic","first_name":"Marko","id":"73e7ecd4-dc85-11ea-9058-88a16394b160"},{"first_name":"Najwa","last_name":"Taib","full_name":"Taib, Najwa"},{"full_name":"Yeates, Anna","last_name":"Yeates","first_name":"Anna"},{"last_name":"Tourte","first_name":"Maxime","full_name":"Tourte, Maxime"},{"last_name":"Gribaldo","first_name":"Simonetta","full_name":"Gribaldo, Simonetta"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"},{"last_name":"Löwe","first_name":"Jan","full_name":"Löwe, Jan"},{"full_name":"Albers, Sonja Verena","last_name":"Albers","first_name":"Sonja Verena"}],"volume":9,"date_updated":"2024-03-19T07:30:53Z","date_created":"2024-03-17T23:00:58Z","scopus_import":"1","article_processing_charge":"No","day":"04","citation":{"mla":"Nußbaum, Phillip, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology, vol. 9, no. 3, Springer Nature, 2024, pp. 698–711, doi:10.1038/s41564-024-01600-5.","short":"P. Nußbaum, D. Kureisaite-Ciziene, D. Bellini, C. Van Der Does, M. Kojic, N. Taib, A. Yeates, M. Tourte, S. Gribaldo, M. Loose, J. Löwe, S.V. Albers, Nature Microbiology 9 (2024) 698–711.","chicago":"Nußbaum, Phillip, Danguole Kureisaite-Ciziene, Dom Bellini, Chris Van Der Does, Marko Kojic, Najwa Taib, Anna Yeates, et al. “Proteins Containing Photosynthetic Reaction Centre Domains Modulate FtsZ-Based Archaeal Cell Division.” Nature Microbiology. Springer Nature, 2024. https://doi.org/10.1038/s41564-024-01600-5.","ama":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, et al. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 2024;9(3):698-711. doi:10.1038/s41564-024-01600-5","ista":"Nußbaum P, Kureisaite-Ciziene D, Bellini D, Van Der Does C, Kojic M, Taib N, Yeates A, Tourte M, Gribaldo S, Loose M, Löwe J, Albers SV. 2024. Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. 9(3), 698–711.","apa":"Nußbaum, P., Kureisaite-Ciziene, D., Bellini, D., Van Der Does, C., Kojic, M., Taib, N., … Albers, S. V. (2024). Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division. Nature Microbiology. Springer Nature. https://doi.org/10.1038/s41564-024-01600-5","ieee":"P. Nußbaum et al., “Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division,” Nature Microbiology, vol. 9, no. 3. Springer Nature, pp. 698–711, 2024."},"publication":"Nature Microbiology","page":"698-711","article_type":"original","date_published":"2024-03-04T00:00:00Z","type":"journal_article","issue":"3","abstract":[{"text":"Cell division in all domains of life requires the orchestration of many proteins, but in Archaea most of the machinery remains poorly characterized. Here we investigate the FtsZ-based cell division mechanism in Haloferax volcanii and find proteins containing photosynthetic reaction centre (PRC) barrel domains that play an essential role in archaeal cell division. We rename these proteins cell division protein B 1 (CdpB1) and CdpB2. Depletions and deletions in their respective genes cause severe cell division defects, generating drastically enlarged cells. Fluorescence microscopy of tagged FtsZ1, FtsZ2 and SepF in CdpB1 and CdpB2 mutant strains revealed an unusually disordered divisome that is not organized into a distinct ring-like structure. Biochemical analysis shows that SepF forms a tripartite complex with CdpB1/2 and crystal structures suggest that these two proteins might form filaments, possibly aligning SepF and the FtsZ2 ring during cell division. Overall our results indicate that PRC-domain proteins play essential roles in FtsZ-based cell division in Archaea.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15118","intvolume":" 9","status":"public","title":"Proteins containing photosynthetic reaction centre domains modulate FtsZ-based archaeal cell division","oa_version":"None"},{"oa_version":"Preprint","status":"public","title":"Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions","intvolume":" 60","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15119","abstract":[{"text":"In this paper we consider an SPDE where the leading term is a second order operator with periodic boundary conditions, coefficients which are measurable in (t,ω) , and Hölder continuous in space. Assuming stochastic parabolicity conditions, we prove Lp((0,T)×Ω,tκdt;Hσ,q(Td)) -estimates. The main novelty is that we do not require p=q . Moreover, we allow arbitrary σ∈R and weights in time. Such mixed regularity estimates play a crucial role in applications to nonlinear SPDEs which is clear from our previous work. To prove our main results we develop a general perturbation theory for SPDEs. Moreover, we prove a new result on pointwise multiplication in spaces with fractional smoothness.","lang":"eng"}],"issue":"1","type":"journal_article","date_published":"2024-02-01T00:00:00Z","article_type":"original","page":"413-430","publication":"Annales de l'institut Henri Poincare Probability and Statistics","citation":{"ista":"Agresti A, Veraar M. 2024. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. 60(1), 413–430.","ieee":"A. Agresti and M. Veraar, “Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions,” Annales de l’institut Henri Poincare Probability and Statistics, vol. 60, no. 1. Institute of Mathematical Statistics, pp. 413–430, 2024.","apa":"Agresti, A., & Veraar, M. (2024). Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/22-AIHP1333","ama":"Agresti A, Veraar M. Stochastic maximal Lp(Lq)-regularity for second order systems with periodic boundary conditions. Annales de l’institut Henri Poincare Probability and Statistics. 2024;60(1):413-430. doi:10.1214/22-AIHP1333","chicago":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut Henri Poincare Probability and Statistics. Institute of Mathematical Statistics, 2024. https://doi.org/10.1214/22-AIHP1333.","mla":"Agresti, Antonio, and Mark Veraar. “Stochastic Maximal Lp(Lq)-Regularity for Second Order Systems with Periodic Boundary Conditions.” Annales de l’institut Henri Poincare Probability and Statistics, vol. 60, no. 1, Institute of Mathematical Statistics, 2024, pp. 413–30, doi:10.1214/22-AIHP1333.","short":"A. Agresti, M. Veraar, Annales de l’institut Henri Poincare Probability and Statistics 60 (2024) 413–430."},"day":"01","article_processing_charge":"No","scopus_import":"1","date_created":"2024-03-17T23:00:58Z","date_updated":"2024-03-19T08:14:17Z","volume":60,"author":[{"orcid":"0000-0002-9573-2962","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","last_name":"Agresti","first_name":"Antonio","full_name":"Agresti, Antonio"},{"full_name":"Veraar, Mark","first_name":"Mark","last_name":"Veraar"}],"publication_status":"published","publisher":"Institute of Mathematical Statistics","department":[{"_id":"JuFi"}],"year":"2024","acknowledgement":"The first author has been partially supported by the Nachwuchsring – Network for the promotion of young scientists – at TU Kaiserslautern. The second author is supported by the VIDI subsidy 639.032.427 of the Netherlands Organisation for Scientific Research (NWO). The authors thank the anonymous referees and Max Sauerbrey for careful reading and helpful suggestions.","language":[{"iso":"eng"}],"doi":"10.1214/22-AIHP1333","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.01274","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2106.01274"]},"month":"02","publication_identifier":{"issn":["0246-0203"]}},{"date_published":"2024-03-12T00:00:00Z","article_type":"original","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"mla":"Habig, Michael, et al. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2316284121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2316284121.","short":"M. Habig, A.V. Grasse, J. Müller, E.H. Stukenbrock, H. Leitner, S. Cremer, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","chicago":"Habig, Michael, Anna V Grasse, Judith Müller, Eva H. Stukenbrock, Hanna Leitner, and Sylvia Cremer. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2316284121.","ama":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2316284121","ista":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. 2024. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2316284121.","apa":"Habig, M., Grasse, A. V., Müller, J., Stukenbrock, E. H., Leitner, H., & Cremer, S. (2024). Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2316284121","ieee":"M. Habig, A. V. Grasse, J. Müller, E. H. Stukenbrock, H. Leitner, and S. Cremer, “Frequent horizontal chromosome transfer between asexual fungal insect pathogens,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024."},"day":"12","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","file":[{"file_id":"15124","relation":"main_file","success":1,"checksum":"f5e871db617b682edc71fcd08670dc81","date_created":"2024-03-19T09:02:57Z","date_updated":"2024-03-19T09:02:57Z","access_level":"open_access","file_name":"2024_PNAS_Habig.pdf","creator":"dernst","file_size":5750361,"content_type":"application/pdf"}],"oa_version":"Published Version","title":"Frequent horizontal chromosome transfer between asexual fungal insect pathogens","status":"public","ddc":["570"],"intvolume":" 121","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14478","abstract":[{"lang":"eng","text":"Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungusMetarhizium robertsiiduring experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment betweenM. robertsiiand another congeneric insect pathogen,M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens."}],"issue":"11","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1073/pnas.2316284121","quality_controlled":"1","project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip"}],"external_id":{"pmid":["38442176"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"month":"03","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_updated":"2024-03-19T09:07:20Z","date_created":"2023-10-31T13:30:00Z","volume":121,"author":[{"full_name":"Habig, Michael","first_name":"Michael","last_name":"Habig"},{"last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"full_name":"Müller, Judith","first_name":"Judith","last_name":"Müller"},{"first_name":"Eva H.","last_name":"Stukenbrock","full_name":"Stukenbrock, Eva H."},{"full_name":"Leitner, Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","first_name":"Hanna","last_name":"Leitner"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia","last_name":"Cremer"}],"publication_status":"published","department":[{"_id":"SyCr"}],"publisher":"Proceedings of the National Academy of Sciences","acknowledgement":"We thank Bernhardt Steinwender, Jorgen Eilenberg, and Nicolai V. Meyling for the fungal strains. We further thank Chengshu Wang for providing the short sequencing reads for M. guizhouense ARESF977 he used for his published genome assembly, and Kristian Ullrich for help in the bioinformatics analysis for methylation pattern in Nanopore reads, and the VBC and the Max Planck Society for the use of their sequencing centers. We thank Barbara Milutinović and Hinrich Schulenburg for discussion, and Tal Dagan and Jens Rolff for comments on a previous version of the manuscript. Fig. 1A was created with BioRender.com. This study received funding by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP) to S.C. and by the German Research Foundation (DFG grant HA9263/1-1) to M.H.","year":"2024","pmid":1,"file_date_updated":"2024-03-19T09:02:57Z","ec_funded":1,"article_number":"e2316284121"},{"type":"journal_article","abstract":[{"lang":"eng","text":"Given a fixed finite metric space (V,μ), the {\\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs.\r\n"}],"_id":"10045","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Generalized minimum 0-extension problem and discrete convexity","ddc":["004"],"status":"public","file":[{"checksum":"e7e83065f7bc18b9c188bf93b5ca5db6","success":1,"date_updated":"2021-09-27T10:54:51Z","date_created":"2021-09-27T10:54:51Z","relation":"main_file","file_id":"10046","content_type":"application/pdf","file_size":603672,"creator":"mdvorak","access_level":"open_access","file_name":"Generalized-0-Ext.pdf"}],"oa_version":"Preprint","scopus_import":"1","keyword":["minimum 0-extension problem","metric labeling problem","discrete metric spaces","metric extensions","computational complexity","valued constraint satisfaction problems","discrete convex analysis","L-convex functions"],"day":"07","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"Mathematical Programming","citation":{"short":"M. Dvorak, V. Kolmogorov, Mathematical Programming (2024).","mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming, 2109.10203, Springer Nature, 2024, doi:10.1007/s10107-024-02064-5.","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02064-5.","ama":"Dvorak M, Kolmogorov V. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. 2024. doi:10.1007/s10107-024-02064-5","ieee":"M. Dvorak and V. Kolmogorov, “Generalized minimum 0-extension problem and discrete convexity,” Mathematical Programming. Springer Nature, 2024.","apa":"Dvorak, M., & Kolmogorov, V. (2024). Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02064-5","ista":"Dvorak M, Kolmogorov V. 2024. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming., 2109.10203."},"article_type":"original","date_published":"2024-03-07T00:00:00Z","article_number":"2109.10203","file_date_updated":"2021-09-27T10:54:51Z","year":"2024","acknowledgement":"We thank the anonymous reviewers for their careful reading of our manuscript and their many insightful comments and suggestions. Open access funding provided by Institute of Science and Technology (IST Austria).","publication_status":"epub_ahead","publisher":"Springer Nature","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"author":[{"first_name":"Martin","last_name":"Dvorak","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","orcid":"0000-0001-5293-214X","full_name":"Dvorak, Martin"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"}],"date_updated":"2024-03-19T08:20:31Z","date_created":"2021-09-27T10:48:23Z","month":"03","publication_identifier":{"eissn":["1436-4646"],"issn":["0025-5610"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2109.10203"]},"oa":1,"quality_controlled":"1","doi":"10.1007/s10107-024-02064-5","language":[{"iso":"eng"}]},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15121","status":"public","title":"Multiplicative auction algorithm for approximate maximum weight bipartite matching","abstract":[{"lang":"eng","text":"We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1-E)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time 0(mE-1), beating the running time of the fastest known approximation algorithm of Duan and Pettie [JACM ’14] that runs in 0(mE-1 log E-1). Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1-E)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is 0(mE-1), where m is the sum of the number of initially existing and inserted edges."}],"type":"journal_article","date_published":"2024-03-06T00:00:00Z","publication":"Mathematical Programming","citation":{"apa":"Zheng, D. W., & Henzinger, M. H. (2024). Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02066-3","ieee":"D. W. Zheng and M. H. Henzinger, “Multiplicative auction algorithm for approximate maximum weight bipartite matching,” Mathematical Programming. Springer Nature, 2024.","ista":"Zheng DW, Henzinger MH. 2024. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming.","ama":"Zheng DW, Henzinger MH. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming. 2024. doi:10.1007/s10107-024-02066-3","chicago":"Zheng, Da Wei, and Monika H Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02066-3.","short":"D.W. Zheng, M.H. Henzinger, Mathematical Programming (2024).","mla":"Zheng, Da Wei, and Monika H. Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming, Springer Nature, 2024, doi:10.1007/s10107-024-02066-3."},"article_type":"original","day":"06","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Zheng, Da Wei","first_name":"Da Wei","last_name":"Zheng"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"13236"}]},"date_updated":"2024-03-19T08:32:32Z","date_created":"2024-03-17T23:00:58Z","year":"2024","acknowledgement":"The first author thanks Chandra Chekuri for useful discussions about this paper. This work was done in part at the University of Vienna. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","publication_status":"epub_ahead","department":[{"_id":"MoHe"}],"publisher":"Springer Nature","ec_funded":1,"doi":"10.1007/s10107-024-02066-3","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.09217","open_access":"1"}],"external_id":{"arxiv":["2301.09217"]},"quality_controlled":"1","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020"},{"grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"}],"month":"03","publication_identifier":{"eissn":["1436-4646"],"issn":["0025-5610"]}},{"intvolume":" 291","title":"Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling","status":"public","_id":"15114","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","type":"journal_article","abstract":[{"text":"As a key liquid organic hydrogen carrier, investigating the decomposition of formic acid (HCOOH) on the Pd (1 1 1) transition metal surface is imperative for harnessing hydrogen energy. Despite a multitude of studies, the major mechanisms and key intermediates involved in the dehydrogenation process of formic acid remain a great topic of debate due to ambiguous adsorbate interactions. In this research, we develop an advanced microkinetic model based on first-principles calculations, accounting for adsorbate–adsorbate interactions. Our study unveils a comprehensive mechanism for the Pd (1 1 1) surface, highlighting the significance of coverage effects in formic acid dehydrogenation. Our findings unequivocally demonstrate that H coverage on the Pd (1 1 1) surface renders formic acid more susceptible to decompose into H2 and CO2 through COOH intermediates. Consistent with experimental results, the selectivity of H2 in the decomposition of formic acid on the Pd (1 1 1) surface approaches 100 %. Considering the influence of H coverage, our kinetic analysis aligns perfectly with experimental values at a temperature of 373 K.","lang":"eng"}],"article_type":"original","citation":{"apa":"Yao, Z., Liu, X., Bunting, R., & Wang, J. (2024). Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. Elsevier. https://doi.org/10.1016/j.ces.2024.119959","ieee":"Z. Yao, X. Liu, R. Bunting, and J. Wang, “Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling,” Chemical Engineering Science, vol. 291. Elsevier, 2024.","ista":"Yao Z, Liu X, Bunting R, Wang J. 2024. Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. 291, 119959.","ama":"Yao Z, Liu X, Bunting R, Wang J. Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. 2024;291. doi:10.1016/j.ces.2024.119959","chicago":"Yao, Zihao, Xu Liu, Rhys Bunting, and Jianguo Wang. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” Chemical Engineering Science. Elsevier, 2024. https://doi.org/10.1016/j.ces.2024.119959.","short":"Z. Yao, X. Liu, R. Bunting, J. Wang, Chemical Engineering Science 291 (2024).","mla":"Yao, Zihao, et al. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” Chemical Engineering Science, vol. 291, 119959, Elsevier, 2024, doi:10.1016/j.ces.2024.119959."},"publication":"Chemical Engineering Science","date_published":"2024-03-04T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"04","department":[{"_id":"MaIb"}],"publisher":"Elsevier","publication_status":"epub_ahead","year":"2024","acknowledgement":"The authors acknowledge the financial support from the National Key Research and Development Project of China (2021YFA1500900, 2022YFE0113800), the National Natural Science Foundation of China (22141001, U21A20298), Zhejiang Innovation Team (2017R5203).","volume":291,"date_created":"2024-03-17T23:00:57Z","date_updated":"2024-03-19T08:47:42Z","author":[{"first_name":"Zihao","last_name":"Yao","full_name":"Yao, Zihao"},{"first_name":"Xu","last_name":"Liu","full_name":"Liu, Xu"},{"orcid":"0000-0001-6928-074X","id":"91deeae8-1207-11ec-b130-c194ad5b50c6","last_name":"Bunting","first_name":"Rhys","full_name":"Bunting, Rhys"},{"first_name":"Jianguo","last_name":"Wang","full_name":"Wang, Jianguo"}],"article_number":"119959","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1016/j.ces.2024.119959","publication_identifier":{"issn":["0009-2509"]},"month":"03"},{"article_number":"e2313162121","file_date_updated":"2024-03-19T10:22:42Z","pmid":1,"acknowledgement":"We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla, and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education, Culture and Science (OCW) and The Netherlands Organization for Scientific Research and from NWO grant OCENW.GROOT.2019.022. This work has received support from the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project (with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from Royal Society and European Research Council Starting Grant. G. Giubertoni kindly thanks to the Care4Bones community and the Collagen Café community for reminding that we do not own the knowledge we create, but it is, rather, a collective resource intended for the advancement of human progress.","year":"2024","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"AnSa"}],"publication_status":"published","related_material":{"record":[{"id":"15126","status":"public","relation":"research_data"}]},"author":[{"first_name":"Giulia","last_name":"Giubertoni","full_name":"Giubertoni, Giulia"},{"full_name":"Feng, Liru","first_name":"Liru","last_name":"Feng"},{"full_name":"Klein, Kevin","last_name":"Klein","first_name":"Kevin"},{"full_name":"Giannetti, Guido","first_name":"Guido","last_name":"Giannetti"},{"full_name":"Rutten, Luco","first_name":"Luco","last_name":"Rutten"},{"full_name":"Choi, Yeji","first_name":"Yeji","last_name":"Choi"},{"last_name":"Van Der Net","first_name":"Anouk","full_name":"Van Der Net, Anouk"},{"full_name":"Castro-Linares, Gerard","first_name":"Gerard","last_name":"Castro-Linares"},{"last_name":"Caporaletti","first_name":"Federico","full_name":"Caporaletti, Federico"},{"full_name":"Micha, Dimitra","last_name":"Micha","first_name":"Dimitra"},{"last_name":"Hunger","first_name":"Johannes","full_name":"Hunger, Johannes"},{"full_name":"Deblais, Antoine","last_name":"Deblais","first_name":"Antoine"},{"full_name":"Bonn, Daniel","last_name":"Bonn","first_name":"Daniel"},{"full_name":"Sommerdijk, Nico","first_name":"Nico","last_name":"Sommerdijk"},{"last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"},{"first_name":"Ioana M.","last_name":"Ilie","full_name":"Ilie, Ioana M."},{"full_name":"Koenderink, Gijsje H.","first_name":"Gijsje H.","last_name":"Koenderink"},{"first_name":"Sander","last_name":"Woutersen","full_name":"Woutersen, Sander"}],"volume":121,"date_created":"2024-03-17T23:00:57Z","date_updated":"2024-03-19T11:41:32Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"03","external_id":{"pmid":["38451946"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1073/pnas.2313162121","language":[{"iso":"eng"}],"type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15116","intvolume":" 121","status":"public","title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","ddc":["550"],"file":[{"access_level":"open_access","file_name":"2024_PNAS_Giubertoni.pdf","file_size":12952586,"content_type":"application/pdf","creator":"dernst","relation":"main_file","file_id":"15125","checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05","success":1,"date_created":"2024-03-19T10:22:42Z","date_updated":"2024-03-19T10:22:42Z"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"12","citation":{"ama":"Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2313162121","apa":"Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., … Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2313162121","ieee":"G. Giubertoni et al., “Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.","ista":"Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2313162121.","short":"G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D. Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2313162121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2313162121.","chicago":"Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten, Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2313162121."},"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_type":"original","date_published":"2024-03-12T00:00:00Z"},{"oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15117","title":"Structure, biophysics, and circuit function of a \"giant\" cortical presynaptic terminal","status":"public","intvolume":" 383","abstract":[{"lang":"eng","text":"The hippocampal mossy fiber synapse, formed between axons of dentate gyrus granule cells and dendrites of CA3 pyramidal neurons, is a key synapse in the trisynaptic circuitry of the hippocampus. Because of its comparatively large size, this synapse is accessible to direct presynaptic recording, allowing a rigorous investigation of the biophysical mechanisms of synaptic transmission and plasticity. Furthermore, because of its placement in the very center of the hippocampal memory circuit, this synapse seems to be critically involved in several higher network functions, such as learning, memory, pattern separation, and pattern completion. Recent work based on new technologies in both nanoanatomy and nanophysiology, including presynaptic patch-clamp recording, paired recording, super-resolution light microscopy, and freeze-fracture and “flash-and-freeze” electron microscopy, has provided new insights into the structure, biophysics, and network function of this intriguing synapse. This brings us one step closer to answering a fundamental question in neuroscience: how basic synaptic properties shape higher network computations."}],"issue":"6687","type":"journal_article","date_published":"2024-03-08T00:00:00Z","publication":"Science","citation":{"chicago":"Vandael, David H, and Peter M Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science. AAAS, 2024. https://doi.org/10.1126/science.adg6757.","mla":"Vandael, David H., and Peter M. Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science, vol. 383, no. 6687, AAAS, 2024, p. eadg6757, doi:10.1126/science.adg6757.","short":"D.H. Vandael, P.M. Jonas, Science 383 (2024) eadg6757.","ista":"Vandael DH, Jonas PM. 2024. Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal. Science. 383(6687), eadg6757.","ieee":"D. H. Vandael and P. M. Jonas, “Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal,” Science, vol. 383, no. 6687. AAAS, p. eadg6757, 2024.","apa":"Vandael, D. H., & Jonas, P. M. (2024). Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. AAAS. https://doi.org/10.1126/science.adg6757","ama":"Vandael DH, Jonas PM. Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. 2024;383(6687):eadg6757. doi:10.1126/science.adg6757"},"article_type":"review","page":"eadg6757","day":"08","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Vandael, David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87","last_name":"Vandael","first_name":"David H"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","full_name":"Jonas, Peter M"}],"date_updated":"2024-03-20T07:42:52Z","date_created":"2024-03-17T23:00:57Z","volume":383,"acknowledgement":"We thank previous students, postdocs, and collaborators, particularly J. Geiger, and (in alphabetical order) H. Alle, J. Bischofberger, C. Borges-Merjane, D. Engel, M. Frotscher, S. Hallermann, M. Heckmann, S. Jamrichova, O. Kim, L. Li, K. Lichter, P. Lin, J. Lübke, Y. Okamoto, C. Pawlu, C. Schmidt-Hieber, N. Spruston, and N. Vyleta for their outstanding experimental contributions. We also thank P. Castillo, J. Geiger, T. Sakaba, S. Siegert, T. Vogels, and J. Watson for critically reading the manuscript, E. Kralli-Beller for text editing, and J. Malikovic and L. Slomianka for useful discussions. We apologize that, due to space constraints, not all relevant papers could be cited.\r\nThis project was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, AdG “GIANTSYN”) and the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein Award; P 36232-B, stand-alone grant), both to P.J.","year":"2024","pmid":1,"publication_status":"published","publisher":"AAAS","department":[{"_id":"PeJo"}],"ec_funded":1,"doi":"10.1126/science.adg6757","language":[{"iso":"eng"}],"external_id":{"pmid":["38452088"]},"quality_controlled":"1","project":[{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","grant_number":"P36232","name":"Mechanisms of GABA release in hippocampal circuits"}],"month":"03","publication_identifier":{"eissn":["1095-9203"]}},{"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2024-03-14T14:14:35Z","ec_funded":1,"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"publisher":"Institute of Science and Technology Austria","year":"2024","date_created":"2024-03-08T15:28:10Z","date_updated":"2024-03-20T09:36:57Z","author":[{"full_name":"Cultrera di Montesano, Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832","first_name":"Sebastiano","last_name":"Cultrera di Montesano"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11660"},{"id":"11658","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"13182"},{"relation":"part_of_dissertation","status":"public","id":"15090"},{"id":"15091","status":"public","relation":"part_of_dissertation"},{"id":"15093","status":"public","relation":"part_of_dissertation"}]},"month":"03","publication_identifier":{"issn":["2663 - 337X"]},"project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"name":"Discretization in Geometry and Dynamics","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316","grant_number":"I4887"},{"grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"degree_awarded":"PhD","supervisor":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"}],"language":[{"iso":"eng"}],"doi":"10.15479/at:ista:15094","alternative_title":["ISTA Thesis"],"type":"dissertation","abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"title":"Persistence and Morse theory for discrete geometric structures","status":"public","ddc":["514","500","516"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"15094","oa_version":"Published Version","file":[{"date_updated":"2024-03-14T08:55:07Z","date_created":"2024-03-14T08:55:07Z","success":1,"checksum":"1e468bfa42a7dcf04d89f4dadc621c87","file_id":"15112","relation":"main_file","creator":"scultrer","file_size":4106872,"content_type":"application/pdf","file_name":"Thesis Sebastiano.pdf","access_level":"open_access"},{"checksum":"bcbd213490f5a7e68855a092bbce93f1","date_created":"2024-03-14T08:56:24Z","date_updated":"2024-03-14T14:14:35Z","file_id":"15113","relation":"source_file","creator":"scultrer","content_type":"application/zip","file_size":4746234,"access_level":"closed","file_name":"Thesis (1).zip"}],"day":"08","article_processing_charge":"No","has_accepted_license":"1","page":"108","citation":{"ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:10.15479/at:ista:15094","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria.","apa":"Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","mla":"Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094."},"date_published":"2024-03-08T00:00:00Z"},{"status":"public","title":"Dynamically maintaining the persistent homology of time series","_id":"15093","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","type":"conference","abstract":[{"lang":"eng","text":"We present a dynamic data structure for maintaining the persistent homology of a time series of real numbers. The data structure supports local operations, including the insertion and deletion of an item and the cutting and concatenating of lists, each in time O(log n + k), in which n counts the critical items and k the changes in the augmented persistence diagram. To achieve this, we design a tailor-made tree structure with an unconventional representation, referred to as banana tree, which may be useful in its own right."}],"page":"243 - 295","citation":{"short":"S. Cultrera di Montesano, H. Edelsbrunner, M.H. Henzinger, L. Ost, in:, D.P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.","mla":"Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11.","chicago":"Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika H Henzinger, and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.” In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11.","ama":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. Dynamically maintaining the persistent homology of time series. In: Woodruff DP, ed. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11","apa":"Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M. H., & Ost, L. (2024). Dynamically maintaining the persistent homology of time series. In D. P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11","ieee":"S. Cultrera di Montesano, H. Edelsbrunner, M. H. Henzinger, and L. Ost, “Dynamically maintaining the persistent homology of time series,” in Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria, VA, USA, 2024, pp. 243–295.","ista":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. 2024. Dynamically maintaining the persistent homology of time series. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete Algorigthms, 243–295."},"publication":"Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)","date_published":"2024-01-04T00:00:00Z","article_processing_charge":"No","day":"04","publisher":"Society for Industrial and Applied Mathematics","editor":[{"last_name":"Woodruff","first_name":"David P.","full_name":"Woodruff, David P."}],"department":[{"_id":"HeEd"},{"_id":"MoHe"}],"publication_status":"published","year":"2024","acknowledgement":"The first and second authors are funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The third author received funding by the European Research Council under the European Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures (MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The fourth author is funded by the Vienna Graduate School on Computational Optimization, FWF project no. W1260-N35.","date_created":"2024-03-08T10:27:39Z","date_updated":"2024-03-20T09:36:56Z","related_material":{"record":[{"id":"15094","relation":"dissertation_contains","status":"public"}]},"author":[{"last_name":"Cultrera di Montesano","first_name":"Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Ost","first_name":"Lara","full_name":"Ost, Lara"}],"ec_funded":1,"project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"_id":"268116B8-B435-11E9-9278-68D0E5697425","grant_number":"Z00342","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"name":"Wittgenstein Award - Monika Henzinger","grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","grant_number":"P33775 ","name":"Fast Algorithms for a Reactive Network Layer"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2311.01115"}],"external_id":{"arxiv":["2311.01115"]},"language":[{"iso":"eng"}],"doi":"10.1137/1.9781611977912.11","conference":{"name":"SODA: Symposium on Discrete Algorigthms","end_date":"2024-01-10","location":"Alexandria, VA, USA","start_date":"2024-01-07"},"publication_identifier":{"eisbn":["9781611977912"]},"month":"01"},{"article_processing_charge":"No","month":"02","day":"07","date_published":"2024-02-07T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv, 2212.03128.","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” arXiv. .","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic alpha complexes. arXiv.","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv.","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d.","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv, 2212.03128.","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.)."},"main_file_link":[{"url":"https://arxiv.org/abs/2212.03128","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2212.03128"]},"publication":"arXiv","abstract":[{"lang":"eng","text":"Motivated by applications in the medical sciences, we study finite chromatic\r\nsets in Euclidean space from a topological perspective. Based on the persistent\r\nhomology for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers that describe the geometric micro- and macro-structure\r\nof how the color classes mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay and alpha complexes, and code that does these\r\ncomputations is provided."}],"type":"preprint","article_number":"2212.03128","related_material":{"record":[{"id":"15094","relation":"dissertation_contains","status":"public"}]},"author":[{"full_name":"Cultrera di Montesano, Sebastiano","first_name":"Sebastiano","last_name":"Cultrera di Montesano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832"},{"id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","last_name":"Draganov","first_name":"Ondrej","full_name":"Draganov, Ondrej"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Saghafian, Morteza","last_name":"Saghafian","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"oa_version":"Preprint","date_updated":"2024-03-20T09:36:56Z","date_created":"2024-03-08T10:13:59Z","_id":"15091","year":"2024","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"HeEd"}],"title":"Chromatic alpha complexes","status":"public","publication_status":"submitted"},{"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15171","status":"public","title":"Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks","abstract":[{"lang":"eng","text":"The brain’s functionality is developed and maintained through synaptic plasticity. As synapses undergo plasticity, they also affect each other. The nature of such ‘co-dependency’ is difficult to disentangle experimentally, because multiple synapses must be monitored simultaneously. To help understand the experimentally observed phenomena, we introduce a framework that formalizes synaptic co-dependency between different connection types. The resulting model explains how inhibition can gate excitatory plasticity while neighboring excitatory–excitatory interactions determine the strength of long-term potentiation. Furthermore, we show how the interplay between excitatory and inhibitory synapses can account for the quick rise and long-term stability of a variety of synaptic weight profiles, such as orientation tuning and dendritic clustering of co-active synapses. In recurrent neuronal networks, co-dependent plasticity produces rich and stable motor cortex-like dynamics with high input sensitivity. Our results suggest an essential role for the neighborly synaptic interaction during learning, connecting micro-level physiology with network-wide phenomena."}],"type":"journal_article","date_published":"2024-03-20T00:00:00Z","citation":{"mla":"Agnes, Everton J., and Tim P. Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience, Springer Nature, 2024, doi:10.1038/s41593-024-01597-4.","short":"E.J. Agnes, T.P. Vogels, Nature Neuroscience (2024).","chicago":"Agnes, Everton J., and Tim P Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience. Springer Nature, 2024. https://doi.org/10.1038/s41593-024-01597-4.","ama":"Agnes EJ, Vogels TP. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. 2024. doi:10.1038/s41593-024-01597-4","ista":"Agnes EJ, Vogels TP. 2024. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience.","ieee":"E. J. Agnes and T. P. Vogels, “Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks,” Nature Neuroscience. Springer Nature, 2024.","apa":"Agnes, E. J., & Vogels, T. P. (2024). Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-024-01597-4"},"publication":"Nature Neuroscience","article_type":"original","article_processing_charge":"Yes (via OA deal)","day":"20","scopus_import":"1","author":[{"first_name":"Everton J.","last_name":"Agnes","full_name":"Agnes, Everton J."},{"last_name":"Vogels","first_name":"Tim P","orcid":"0000-0003-3295-6181","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","full_name":"Vogels, Tim P"}],"date_updated":"2024-03-25T07:04:05Z","date_created":"2024-03-24T23:01:00Z","acknowledgement":"We thank C. Currin, B. Podlaski and the members of the Vogels group for fruitful discussions. E.J.A. and T.P.V. were supported by a Research Project Grant from the Leverhulme Trust (RPG-2016-446; TPV), a Sir Henry Dale Fellowship from the Wellcome Trust and the Royal Society (WT100000; T.P.V.), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; T.P.V.) and a European Research Council Consolidator Grant (SYNAPSEEK, 819603; T.P.V.). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. Open access funding provided by University of Basel.","year":"2024","department":[{"_id":"TiVo"}],"publisher":"Springer Nature","publication_status":"epub_ahead","ec_funded":1,"doi":"10.1038/s41593-024-01597-4","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41593-024-01597-4"}],"oa":1,"project":[{"grant_number":"819603","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning."}],"quality_controlled":"1","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"month":"03"}]